5Z16 | pdb_00005z16

A novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb5Z16/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-12-25 Released: 2019-02-20 
• Deposition Author(s): Song, P., Huang, S.P., Wang, P., Zhu, G.P.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

A novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii

Wang, P., Zhu, G.P., Song, P., Huang, S.P.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 167.44 kDa 
• Atom Count: 11,788 
• Modeled Residue Count: 1,474 
• Deposited Residue Count: 1,502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase	A, B	751	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  icd_2, A7M79_07490, A7N09_00330, APD06_04285, APD31_03935, AZE33_14960, B4R90_02155, B9X91_18100, B9X95_15090, BGC29_03310, BWP00_11420, CAS83_18605, CAT78_13885, CEJ63_01165, CHH39_15940, CHQ89_08020, IX87_09060, LV38_02052 EC: 1.1.1.42

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.161	α = 90
b = 137.161	β = 90
c = 238.132	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Song, P., Huang, S.P., Wang, P., Zhu, G.P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570010, 31170005, 31400003

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description