4ROS | pdb_00004ros

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

• PDB DOI: https://doi.org/10.2210/pdb4ROS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methylorubrum extorquens PA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-28 Released: 2014-12-17 
• Deposition Author(s): Gonzalez, J.M., Marti-Arbona, R., Unkefer, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 34.45 kDa 
• Atom Count: 2,515 
• Modeled Residue Count: 318 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A	320	Methylorubrum extorquens PA1	Mutation(s): 0  Gene Names: mdh, Mext_1643 EC: 1.1.1.37
UniProt
Find proteins for A9W386 (Methylorubrum extorquens (strain PA1)) Explore A9W386  Go to UniProtKB:  A9W386

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR	E [auth A]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
OAA	D [auth A]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.396	α = 90
b = 108.396	β = 90
c = 104.014	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Gonzalez, J.M., Marti-Arbona, R., Unkefer, C.J.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2018-06-06
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations