2OMD | pdb_00002omd

Crystal structure of molybdopterin converting factor subunit 2 (aq_2181) from aquifex aeolicus VF5

• PDB DOI: https://doi.org/10.2210/pdb2OMD/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-01-22 Released: 2008-01-29 
• Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of molybdopterin converting factor subunit 2 (aq_2181) from aquifex aeolicus VF5

Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.69 kDa 
• Atom Count: 2,675 
• Modeled Residue Count: 280 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin-converting factor subunit 2	A, B	154	Aquifex aeolicus VF5	Mutation(s): 0  EC: 2.8.1.12
UniProt
Find proteins for O67928 (Aquifex aeolicus (strain VF5)) Explore O67928  Go to UniProtKB:  O67928

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	F [auth A], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.995	α = 90
b = 119.995	β = 90
c = 125.804	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-29 
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-01-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations