6C0Z | pdb_00006c0z

Crystal structure of Efga from Methylobacterium extorquens in complex with formaldehyde

• PDB DOI: https://doi.org/10.2210/pdb6C0Z/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methylorubrum extorquens DSM 13060
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-03 Released: 2019-01-16 
• Deposition Author(s): Shamoo, Y., Davlieva, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Efga form Methylobacterium extorquens in complex with formaldehyde

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

Macromolecule Content 

• Total Structure Weight: 68.13 kDa 
• Atom Count: 4,338 
• Modeled Residue Count: 548 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Efga	A [auth B], B [auth A], C, D	164	Methylorubrum extorquens DSM 13060	Mutation(s): 0  Gene Names: MetexDRAFT_1898
UniProt
Find proteins for P0DX96 (Methylorubrum extorquens (strain PA1)) Explore P0DX96  Go to UniProtKB:  P0DX96

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
21H	F [auth A], G [auth C], H [auth D]	oxydimethanol C2 H6 O3 ARZLUCYKIWYSHR-UHFFFAOYSA-N
FMT	E [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.059	α = 90
b = 72.063	β = 90
c = 104.555	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
	United States	--

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description