3U02 | pdb_00003u02

Crystal Structure of the tRNA modifier TiaS from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR225

PDB DOI: https://doi.org/10.2210/pdb3U02/pdb

Classification: TRANSCRIPTION
Organism(s): Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-09-28 Released: 2011-11-02
Deposition Author(s): Kuzin, A., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.242 (Depositor), 0.239 (DCC)
R-Value Work:
0.179 (Depositor), 0.175 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the tRNA modifier TiaS from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR225

Kuzin, A., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 119.58 kDa
Atom Count: 8,052
Modeled Residue Count: 933
Deposited Residue Count: 1,008
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcription-associated protein TFIIS	A, B, C, D	252	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF1855 EC: 6.3.4.22
UniProt
Find proteins for Q8TZX0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZX0 Go to UniProtKB: Q8TZX0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain P [auth B] SDF format, chain I [auth A] MOL2 format, chain W [auth D] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] mmCIF format, chain W [auth D] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A]	I [auth A], P [auth B], W [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
TPO Query on TPO	A, B, C, D	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.242 (Depositor), 0.239 (DCC)
R-Value Work: 0.179 (Depositor), 0.175 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.147	α = 90
b = 135.805	β = 93.76
c = 77.269	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-11-02

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2011-11-02
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary