6BWS | pdb_00006bws

Crystal structure of Efga from Methylobacterium extorquens

• PDB DOI: https://doi.org/10.2210/pdb6BWS/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methylorubrum extorquens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-15 Released: 2019-01-16 
• Deposition Author(s): Shamoo, Y., Davlieva, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Efga from Methylobacterium extorquens

Shamoo, Y., Davlieva, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.85 kDa 
• Atom Count: 4,390 
• Modeled Residue Count: 548 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycolate utilization protein	A, B, C, D	164	Methylorubrum extorquens	Mutation(s): 0  Gene Names: BV511_11735
UniProt
Find proteins for P0DX96 (Methylorubrum extorquens (strain PA1)) Explore P0DX96  Go to UniProtKB:  P0DX96

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.817	α = 90
b = 72	β = 90
c = 105.176	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Shamoo, Y., Davlieva, M.

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description