4ZN6 | pdb_00004zn6

X-ray Crystal Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb4ZN6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baumannii AB307-0294
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-04 Released: 2015-05-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystal Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii

Fairman, J.W., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.6 kDa 
• Atom Count: 6,462 
• Modeled Residue Count: 780 
• Deposited Residue Count: 812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B	406	Acinetobacter baumannii AB307-0294	Mutation(s): 0  Gene Names: dxr, ABBFA_001475 EC: 1.1.1.267
UniProt
Find proteins for B7H1U5 (Acinetobacter baumannii (strain AB307-0294)) Explore B7H1U5  Go to UniProtKB:  B7H1U5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34ZN6

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.27	α = 90
b = 65.43	β = 92.09
c = 121.68	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description