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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.276 (Depositor), 0.275 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

A novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii

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

To be published.

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

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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... 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	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.276 (Depositor), 0.275 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-02-20

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.