1PHQ | pdb_00001phq

Crystal structure of KDO8P synthase in its binary complex with substrate analog E-FPEP

• PDB DOI: https://doi.org/10.2210/pdb1PHQ/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-29 Released: 2004-07-13 
• Deposition Author(s): Vainer, R., Adir, N., Baasov, T., Belakhov, V., Rabkin, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.322 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Crystallographic Analysis of the Phosphoenol Pyruvate Binding Site in E. Coli KDO8P Synthase

Vainer, R., Adir, N., Baasov, T., Belakhov, V., Rabkin, E.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 31.06 kDa 
• Atom Count: 2,127 
• Modeled Residue Count: 272 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A	284	Escherichia coli	Mutation(s): 0  Gene Names: KDSA EC: 2.5.1.55
UniProt
Find proteins for P0A715 (Escherichia coli (strain K12)) Explore P0A715  Go to UniProtKB:  P0A715

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPE	B [auth A]	3-FLUORO-2-(PHOSPHONOOXY)PROPANOIC ACID C3 H6 F O6 P BNOCDEBUFVJMQI-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.322 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.783	α = 90
b = 117.783	β = 90
c = 117.783	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-13 
Deposition Author(s): Vainer, R., Adir, N., Baasov, T., Belakhov, V., Rabkin, E.

Revision History  

• Version 1.0: 2004-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description