3RPD

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.

Cuff, M.E.Li, H.Hatzos-Skintges, C.Tesar, C.Bearden, J.Clancy, A.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine synthase (B12-independent)
A, B
357N/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
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MSE
Query on MSE

Download SDF File 
Download CCD File 
A, B
SELENOMETHIONINE
C5 H11 N O2 Se
RJFAYQIBOAGBLC-BYPYZUCNSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.099α = 90.00
b = 89.371β = 92.45
c = 86.526γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
Omodel building
REFMACrefinement
HKL-3000phasing
DENZOdata reduction
DMphasing
MLPHAREphasing
RESOLVEphasing
SCALEPACKdata scaling
SBC-Collectdata collection
ARP/wARPmodel building
PDB_EXTRACTdata extraction
HKL-3000data reduction
SHELXDphasing
SOLVEphasing
CCP4phasing
SHELXEmodel building
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description