5VRC | pdb_00005vrc

Crystal structure for Methylobacterium extorquens PqqC (truncation of natural CD fusion)

• PDB DOI: https://doi.org/10.2210/pdb5VRC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methylorubrum extorquens AM1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-10 Released: 2018-05-16 
• Deposition Author(s): Evans III, R.L., Wilmot, C.M., Esler, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structures for Methylobacterium extorquens PqqC from the CD natural fusion and the C truncation

Evans III, R.L., Esler, M.A., Latham, J.A., Klinman, J.P., Wilmot, C.M.

Not Published 

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)

Biological Assembly Evidence: homology, native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 127.37 kDa 
• Atom Count: 7,057 
• Modeled Residue Count: 904 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional coenzyme PQQ synthesis protein C/D	A, B, C, D	280	Methylorubrum extorquens AM1	Mutation(s): 0  Gene Names: pqqCD, MexAM1_META1p1749 EC: 1.3.3.11
UniProt
Find proteins for Q49150 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore Q49150  Go to UniProtKB:  Q49150

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.501	α = 90
b = 114.185	β = 90
c = 145.403	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Evans III, R.L., Wilmot, C.M., Esler, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM66569 (C.M.W.)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-118117 (J.P.K.)

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description