3IEM | pdb_00003iem

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog

PDB DOI: https://doi.org/10.2210/pdb3IEM/pdb
NAKB: 3IEM

Classification: HYDROLASE/RNA
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., Kuramitus, S., Yokoyama, S., Masui, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.257 (Depositor), 0.252 (DCC)
R-Value Work:
0.213 (Depositor), 0.208 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog

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

To be published.

Macromolecule Content

Total Structure Weight: 213.74 kDa
Atom Count: 14,354
Modeled Residue Count: 1,759
Deposited Residue Count: 1,784
Unique protein chains: 1
Unique nucleic acid 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

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Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3')	E [auth G] F [auth H] G [auth I] H [auth J] I [auth K] E [auth G], F [auth H], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N], M [auth O], N [auth P]	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain YA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain YA [auth B]	YA [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain YA [auth B] Interactions & Density Focus chain YA [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain DC [auth K] SDF format, chain EB [auth C] SDF format, chain GB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain MB [auth C] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth D] SDF format, chain SA [auth B] SDF format, chain SB [auth D] SDF format, chain T [auth A] SDF format, chain TB [auth D] SDF format, chain U [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WB [auth D] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YB [auth D] SDF format, chain Z [auth A] SDF format, chain ZB [auth D] SDF format, chain XB [auth D] SDF format, chain X [auth A] SDF format, chain V [auth A] SDF format, chain UB [auth D] SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain S [auth A] SDF format, chain O [auth A] SDF format, chain MA [auth B] SDF format, chain LB [auth C] SDF format, chain LA [auth B] SDF format, chain JA [auth B] SDF format, chain HB [auth C] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FB [auth C] SDF format, chain CC [auth J] SDF format, chain CA [auth A] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth K] MOL2 format, chain EB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth D] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth D] MOL2 format, chain XB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain V [auth A] MOL2 format, chain UB [auth D] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain CC [auth J] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain DC [auth K] mmCIF format, chain EB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain MB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth D] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TB [auth D] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain VB [auth D] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth D] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth D] mmCIF format, chain Z [auth A] mmCIF format, chain ZB [auth D] mmCIF format, chain XB [auth D] mmCIF format, chain X [auth A] mmCIF format, chain V [auth A] mmCIF format, chain UB [auth D] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain CC [auth J] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] BB [auth C] CA [auth A] CB [auth C] AA [auth A], BA [auth A], BB [auth C], CA [auth A], CB [auth C], CC [auth J], DA [auth A], DB [auth C], DC [auth K], EB [auth C], FB [auth C], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth B], LB [auth C], MA [auth B], MB [auth C], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], PB [auth D], Q [auth A], QA [auth B], QB [auth D], R [auth A], RA [auth B], RB [auth D], S [auth A], SA [auth B], SB [auth D], T [auth A], TA [auth B], TB [auth D], U [auth A], UA [auth B], UB [auth D], V [auth A], VA [auth B], VB [auth D], W [auth A], WA [auth B], WB [auth D], X [auth A], XA [auth B], XB [auth D], Y [auth A], YB [auth D], Z [auth A], ZB [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain CC [auth J] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth K] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZB [auth D] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain CC [auth J] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth K] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZB [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain NB [auth C] SDF format, chain OB [auth C] SDF format, chain ZA [auth B] SDF format, chain FA [auth A] SDF format, chain BC [auth D] SDF format, chain AC [auth D] SDF format, chain AB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain OB [auth C] MOL2 format, chain ZA [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain BC [auth D] MOL2 format, chain AC [auth D] MOL2 format, chain AB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain OB [auth C] mmCIF format, chain ZA [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain BC [auth D] mmCIF format, chain AC [auth D] mmCIF format, chain AB [auth B]	AB [auth B] AC [auth D] BC [auth D] EA [auth A] FA [auth A] AB [auth B], AC [auth D], BC [auth D], EA [auth A], FA [auth A], NB [auth C], OB [auth C], ZA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain AC [auth D] Focus chain BC [auth D] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain AC [auth D] Focus chain BC [auth D] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.257 (Depositor), 0.252 (DCC)
R-Value Work: 0.213 (Depositor), 0.208 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.694	α = 90
b = 146.441	β = 110.37
c = 119.975	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
XFIT	data reduction
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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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: 2023-11-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description