1O4T | pdb_00001o4t

Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1O4T/pdb

• Classification: LYASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-07-03 Released: 2003-07-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.217 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution

Schwarzenbacher, R., von Delft, F., Jaroszewski, L., Abdubek, P., Ambing, E., Biorac, T., Brinen, L.S., Canaves, J.M., Cambell, J., Chiu, H.J., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Eshagi, S., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Hampton, E., Karlak, C., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., McMullan, D., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Quijano, K., Robb, A., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X., West, B., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2004) Proteins 56: 392-395

• PubMed: 15211523 
• DOI: https://doi.org/10.1002/prot.20016
• Primary Citation of Related Structures:  
  1O4T

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Organizational Affiliation: 
• Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.79 kDa 
• Atom Count: 1,993 
• Modeled Residue Count: 230 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative oxalate decarboxylase	A, B	133	Thermotoga maritima	Mutation(s): 0  Gene Names: TM1287
UniProt
Find proteins for Q9X113 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X113  Go to UniProtKB:  Q9X113

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OXL	D [auth A], F [auth B]	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.217 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31O4T

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.132	α = 90
b = 49.738	β = 123.73
c = 69.547	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-07-18
  Changes: Data collection, Database references
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2023-09-20
  Changes: Data collection, Refinement description