2A2J | pdb_00002a2j

Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb2A2J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-06-22 Released: 2005-08-23 
• Deposition Author(s): Pedelacq, J.-D., Rho, B.-S., Kim, C.-Y., Waldo, G.S., Lekin, T.P., Segelke, B.W., Rupp, B., Hung, L.-W., Kim, S.-I., Terwilliger, T.C., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.260 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis.

Pedelacq, J.-D., Rho, B.-S., Kim, C.-Y., Waldo, G.S., Lekin, T.P., Segelke, B.W., Rupp, B., Hung, L.-W., Kim, S.-I., Terwilliger, T.C.

(2005) Proteins 62: 563-569

• PubMed: 16374842 
• DOI: https://doi.org/10.1002/prot.20824
• Primary Citation Related Structures: 
  2A2J


• PubMed Abstract: 
  

  The three-dimensional structure of Rv2607, a putative pyridoxine 5'-phosphate oxidase (PNPOx) from Mycobacterium tuberculosis, has been determined by X-ray crystallography to 2.5 A resolution. Rv2607 has a core domain similar to known PNPOx structures with a flavin mononucleotide (FMN) cofactor. Electron density for two FMN at the dimer interface is weak despite the bright yellow color of the protein solution and crystal. The shape and size of the putative binding pocket is markedly different from that of members of the PNPOx family, which may indicate some significant changes in the FMN binding mode of this protein relative to members of the family.

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Organizational Affiliation: 
• Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA. [e-mail]

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: 55.21 kDa 
• Atom Count: 3,281 
• Modeled Residue Count: 406 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxamine 5'-phosphate oxidase	A, B	246	Mycobacterium tuberculosis	Mutation(s): 1  EC: 1.4.3.5
UniProt
Find proteins for P9WIJ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIJ1  Go to UniProtKB:  P9WIJ1

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.260 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.609	α = 90
b = 91.108	β = 90
c = 92.992	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-23 
Deposition Author(s): Pedelacq, J.-D., Rho, B.-S., Kim, C.-Y., Waldo, G.S., Lekin, T.P., Segelke, B.W., Rupp, B., Hung, L.-W., Kim, S.-I., Terwilliger, T.C., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

Revision History  

• Version 1.0: 2005-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary