6DAM

Crystal structure of lanthanide-dependent methanol dehydrogenase XoxF from Methylomicrobium buryatense 5G

  • Classification: OXIDOREDUCTASE

  • Deposited: 2018-05-01 Released: 2018-09-05 
  • Deposition Author(s): Deng, Y., Ro, S.Y., Rosenzweig, A.C.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C.

Deng, Y.W.Ro, S.Y.Rosenzweig, A.C.

(2018) J. Biol. Inorg. Chem. 23: 1037-1047


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lanthanide-dependent methanol dehydrogenase XoxF
A
617N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LA
Query on LA

Download SDF File 
Download CCD File 
A
LANTHANUM (III) ION
La
CZMAIROVPAYCMU-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PQQ
Query on PQQ

Download SDF File 
Download CCD File 
A
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 55.347α = 90.00
b = 92.283β = 90.00
c = 191.772γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM118035

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references