3VML | pdb_00003vml

Chimera 3-isopropylmalate dehydrogenase between Shewanella oneidensis MR-1 (O) and Shewanella benthica DB21 MT-2 (M) from N-terminal: 20% O middle 70% M residual 10% O

• PDB DOI: https://doi.org/10.2210/pdb3VML/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shewanella oneidensis MR-1, Shewanella benthica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-13 Released: 2012-12-26 
• Deposition Author(s): Nagae, T., Watanabe, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structure analysis of chimeric 3-isopropylmalate dehydrogenase between the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1

Hamajima, Y., Nagae, T., Watanabe, N., Kato, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 40.96 kDa 
• Atom Count: 3,280 
• Modelled Residue Count: 363 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A	375	Shewanella oneidensis MR-1, Shewanella benthica	Mutation(s): 0  Gene Names: leuB, SO_4235 EC: 1.1.1.85
UniProt
Find proteins for D2YZL2 (Shewanella benthica) Explore D2YZL2  Go to UniProtKB:  D2YZL2
Find proteins for Q8E9N3 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8E9N3  Go to UniProtKB:  Q8E9N3
UniProt Groups	Q8E9N3D2YZL2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPM	B [auth A]	3-ISOPROPYLMALIC ACID C7 H12 O5 RNQHMTFBUSSBJQ-CRCLSJGQSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.008	α = 90
b = 107.523	β = 90
c = 83.109	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Nagae, T., Watanabe, N.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description