5YDB | pdb_00005ydb

Crystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter baumannii with dehydroquinic acid at 1.76 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5YDB/pdb

• Classification: LYASE
• Organism(s): Acinetobacter baumannii ATCC 17978
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-12 Released: 2017-09-20 
• Deposition Author(s): Iqbal, N., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter baumannii with dehydroquinic acid at 1.76 Angstrom resolution

Iqbal, N., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.59 kDa 
• Atom Count: 4,742 
• Modeled Residue Count: 580 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B, C, D	148	Acinetobacter baumannii ATCC 17978	Mutation(s): 0  Gene Names: aroQ, A1S_2009 EC: 4.2.1.10
UniProt
Find proteins for A3M692 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M692  Go to UniProtKB:  A3M692

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DQA	F [auth A], H [auth B], J [auth C], L [auth D]	1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID C7 H10 O6 WVMWZWGZRAXUBK-SYTVJDICSA-N
NA	E [auth A], G [auth B], I [auth C], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.117	α = 90
b = 139.117	β = 90
c = 79.587	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Iqbal, N., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2018-07-04
  Changes: Data collection
• Version 1.2: 2018-07-11
  Changes: Data collection
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description