4NAR | pdb_00004nar

Crystal Structure of the Q9WYS3 protein from Thermotoga maritima. Northeast Structural Genomics Consortium Target VR152

• PDB DOI: https://doi.org/10.2210/pdb4NAR/pdb

• Classification: ISOMERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-22 Released: 2013-11-06 
• Deposition Author(s): Vorobiev, S., Lew, S., Seetharaman, J., Chi, Y., Xiao, R., Maglaqui, M., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal Structure of the Q9WYS3 protein from Thermotoga maritima.

Vorobiev, S., Lew, S., Seetharaman, J., Chi, Y., Xiao, R., Maglaqui, M., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.01 kDa 
• Atom Count: 3,585 
• Modeled Residue Count: 420 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uronate isomerase	A	435	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: Tmari_0439, TM_0442
UniProt
Find proteins for Q9WYS3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYS3  Go to UniProtKB:  Q9WYS3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.903	α = 90
b = 144.605	β = 90
c = 49.612	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Vorobiev, S., Lew, S., Seetharaman, J., Chi, Y., Xiao, R., Maglaqui, M., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary