3IEL | pdb_00003iel

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP

PDB DOI: https://doi.org/10.2210/pdb3IEL/pdb

Classification: HYDROLASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-07-23 Released: 2010-07-28
Deposition Author(s): Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.

To be published.

Macromolecule Content

Total Structure Weight: 200.87 kDa
Atom Count: 14,251
Modeled Residue Count: 1,724
Deposited Residue Count: 1,724
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease TTHA0252	A, B, C, D	431	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA0252 EC: 3.1
UniProt
Find proteins for Q5SLP1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP1 Go to UniProtKB: Q5SLP1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLP1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download:Ideal Coordinates CCD File SDF format, chain KD [auth D] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain RC [auth C] SDF format, chain LA [auth A] MOL2 format, chain KD [auth D] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain RC [auth C] MOL2 format, chain LA [auth A] mmCIF format, chain KD [auth D] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain RC [auth C] mmCIF format, chain LA [auth A]	KD [auth D] LA [auth A] MA [auth A] NA [auth A] OB [auth B] KD [auth D], LA [auth A], MA [auth A], NA [auth A], OB [auth B], PB [auth B], RC [auth C]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain KD [auth D] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain RC [auth C]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain KA [auth A] SDF format, chain NB [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain NB [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain NB [auth B]	KA [auth A], NB [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain KA [auth A] Focus chain NB [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AD [auth D] SDF format, chain BC [auth C] SDF format, chain BD [auth D] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain CC [auth C] SDF format, chain CD [auth D] SDF format, chain DA [auth A] SDF format, chain DC [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain ED [auth D] SDF format, chain F [auth A] SDF format, chain FB [auth B] SDF format, chain FC [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain GC [auth C] SDF format, chain GD [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain HC [auth C] SDF format, chain HD [auth D] SDF format, chain IA [auth A] SDF format, chain IB [auth B] SDF format, chain IC [auth C] SDF format, chain ID [auth D] SDF format, chain J [auth A] SDF format, chain JB [auth B] SDF format, chain JC [auth C] SDF format, chain K [auth A] SDF format, chain KB [auth B] SDF format, chain KC [auth C] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain MC [auth C] SDF format, chain N [auth A] SDF format, chain NC [auth C] SDF format, chain O [auth A] SDF format, chain OC [auth C] SDF format, chain PC [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QC [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain UC [auth D] SDF format, chain VA [auth B] SDF format, chain VC [auth D] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain XC [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YB [auth C] SDF format, chain YC [auth D] SDF format, chain ZB [auth C] SDF format, chain ZC [auth D] SDF format, chain ZA [auth B] SDF format, chain Z [auth A] SDF format, chain WC [auth D] SDF format, chain WB [auth C] SDF format, chain WA [auth B] SDF format, chain VB [auth C] SDF format, chain V [auth A] SDF format, chain TB [auth C] SDF format, chain RA [auth B] SDF format, chain P [auth A] SDF format, chain M [auth A] SDF format, chain LC [auth C] SDF format, chain L [auth A] SDF format, chain JD [auth D] SDF format, chain JA [auth A] SDF format, chain I [auth A] SDF format, chain FD [auth D] SDF format, chain FA [auth A] SDF format, chain EC [auth C] SDF format, chain EB [auth B] SDF format, chain DD [auth D] SDF format, chain DB [auth B] SDF format, chain BB [auth B] SDF format, chain BA [auth A] SDF format, chain AC [auth C] SDF format, chain AB [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AD [auth D] MOL2 format, chain BC [auth C] MOL2 format, chain BD [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth C] MOL2 format, chain CD [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DC [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain ED [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain GC [auth C] MOL2 format, chain GD [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain HC [auth C] MOL2 format, chain HD [auth D] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain IC [auth C] MOL2 format, chain ID [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain JC [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth C] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain MC [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NC [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OC [auth C] MOL2 format, chain PC [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QC [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain UC [auth D] MOL2 format, chain VA [auth B] MOL2 format, chain VC [auth D] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain XC [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth C] MOL2 format, chain YC [auth D] MOL2 format, chain ZB [auth C] MOL2 format, chain ZC [auth D] MOL2 format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain WC [auth D] MOL2 format, chain WB [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain V [auth A] MOL2 format, chain TB [auth C] MOL2 format, chain RA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LC [auth C] MOL2 format, chain L [auth A] MOL2 format, chain JD [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain FD [auth D] MOL2 format, chain FA [auth A] MOL2 format, chain EC [auth C] MOL2 format, chain EB [auth B] MOL2 format, chain DD [auth D] MOL2 format, chain DB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain AC [auth C] MOL2 format, chain AB [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AD [auth D] mmCIF format, chain BC [auth C] mmCIF format, chain BD [auth D] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain CC [auth C] mmCIF format, chain CD [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain DC [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain ED [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain FC [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain GC [auth C] mmCIF format, chain GD [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain HC [auth C] mmCIF format, chain HD [auth D] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain IC [auth C] mmCIF format, chain ID [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain JC [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain KC [auth C] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain MC [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NC [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OC [auth C] mmCIF format, chain PC [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain QC [auth C] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth C] mmCIF format, chain UC [auth D] mmCIF format, chain VA [auth B] mmCIF format, chain VC [auth D] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain XB [auth C] mmCIF format, chain XC [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain YB [auth C] mmCIF format, chain YC [auth D] mmCIF format, chain ZB [auth C] mmCIF format, chain ZC [auth D] mmCIF format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain WC [auth D] mmCIF format, chain WB [auth C] mmCIF format, chain WA [auth B] mmCIF format, chain VB [auth C] mmCIF format, chain V [auth A] mmCIF format, chain TB [auth C] mmCIF format, chain RA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LC [auth C] mmCIF format, chain L [auth A] mmCIF format, chain JD [auth D] mmCIF format, chain JA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain FD [auth D] mmCIF format, chain FA [auth A] mmCIF format, chain EC [auth C] mmCIF format, chain EB [auth B] mmCIF format, chain DD [auth D] mmCIF format, chain DB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AC [auth C] mmCIF format, chain AB [auth B]	AA [auth A] AB [auth B] AC [auth C] AD [auth D] BA [auth A] AA [auth A], AB [auth B], AC [auth C], AD [auth D], BA [auth A], BB [auth B], BC [auth C], BD [auth D], CA [auth A], CB [auth B], CC [auth C], CD [auth D], DA [auth A], DB [auth B], DC [auth C], DD [auth D], E [auth A], EA [auth A], EB [auth B], EC [auth C], ED [auth D], F [auth A], FA [auth A], FB [auth B], FC [auth C], FD [auth D], G [auth A], GA [auth A], GB [auth B], GC [auth C], GD [auth D], H [auth A], HA [auth A], HB [auth B], HC [auth C], HD [auth D], I [auth A], IA [auth A], IB [auth B], IC [auth C], ID [auth D], J [auth A], JA [auth A], JB [auth B], JC [auth C], JD [auth D], K [auth A], KB [auth B], KC [auth C], L [auth A], LB [auth B], LC [auth C], M [auth A], MB [auth B], MC [auth C], N [auth A], NC [auth C], O [auth A], OC [auth C], P [auth A], PC [auth C], Q [auth A], QA [auth B], QC [auth C], R [auth A], RA [auth B], S [auth A], SA [auth B], SB [auth C], T [auth A], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], W [auth A], WA [auth B], WB [auth C], WC [auth D], X [auth A], XA [auth B], XB [auth C], XC [auth D], Y [auth A], YA [auth B], YB [auth C], YC [auth D], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AD [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain BD [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain CD [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain DD [auth D] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain ED [auth D] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain FD [auth D] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth C] Focus chain GD [auth D] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain HC [auth C] Focus chain HD [auth D] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain IC [auth C] Focus chain ID [auth D] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain JC [auth C] Focus chain JD [auth D] Focus chain K [auth A] Focus chain KB [auth B] Focus chain KC [auth C] Focus chain L [auth A] Focus chain LB [auth B] Focus chain LC [auth C] Focus chain M [auth A] Focus chain MB [auth B] Focus chain MC [auth C] Focus chain N [auth A] Focus chain NC [auth C] Focus chain O [auth A] Focus chain OC [auth C] Focus chain P [auth A] Focus chain PC [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QC [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain XC [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain YC [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZC [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain LD [auth D] SDF format, chain MD [auth D] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain RB [auth B] SDF format, chain TC [auth C] SDF format, chain SC [auth C] SDF format, chain QB [auth B] MOL2 format, chain LD [auth D] MOL2 format, chain MD [auth D] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain TC [auth C] MOL2 format, chain SC [auth C] MOL2 format, chain QB [auth B] mmCIF format, chain LD [auth D] mmCIF format, chain MD [auth D] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain RB [auth B] mmCIF format, chain TC [auth C] mmCIF format, chain SC [auth C] mmCIF format, chain QB [auth B]	LD [auth D] MD [auth D] OA [auth A] PA [auth A] QB [auth B] LD [auth D], MD [auth D], OA [auth A], PA [auth A], QB [auth B], RB [auth B], SC [auth C], TC [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain LD [auth D] Focus chain MD [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SC [auth C] Focus chain TC [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.222 (Depositor), 0.222 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.238	α = 90
b = 146.677	β = 110.11
c = 120.349	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
XFIT	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description