4IJK | pdb_00004ijk

Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Helicobacter pylori 26695

• PDB DOI: https://doi.org/10.2210/pdb4IJK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-21 Released: 2013-01-09 
• Deposition Author(s): Hou, J., Osinski, T., Zheng, H., Shumilin, I., Shabalin, I.G., Shatsman, S., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.272 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Helicobacter pylori 26695

Hou, J., Osinski, T., Zheng, H., Shumilin, I., Shabalin, I.G., Shatsman, S., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 117.8 kDa 
• Atom Count: 6,901 
• Modeled Residue Count: 927 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ketoacyl-acyl carrier protein reductase (FabG)	A, B, C, D	271	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP0561, HP_0561 EC: 1.1.1.100
UniProt
Find proteins for O25286 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25286  Go to UniProtKB:  O25286

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.272 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m3d30p

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.168	α = 90
b = 114.642	β = 90
c = 69.501	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Hou, J., Osinski, T., Zheng, H., Shumilin, I., Shabalin, I.G., Shatsman, S., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Refinement description