4ROS

Crystal structure of Methylobacterium extorquens malate dehydrogenase complexed with oxaloacetate and adenosine-5-diphosphoribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of Methylobacterium extorquens malate dehydrogenase complexed with oxaloacetate and adenosine-5-diphosphoribose

Gonzalez, J.M.Marti-Arbona, R.Unkefer, C.J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase
A
320Methylobacterium extorquens (strain PA1)Mutation(s): 0 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for A9W386 (Methylobacterium extorquens (strain PA1))
Go to UniProtKB:  A9W386
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download SDF File 
Download CCD File 
A
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
OAA
Query on OAA

Download SDF File 
Download CCD File 
A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.396α = 90.00
b = 108.396β = 90.00
c = 104.014γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
ADSCdata collection
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Advisory, Data collection, Derived calculations