2QKF | pdb_00002qkf

Crystal structure of 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis

• PDB DOI: https://doi.org/10.2210/pdb2QKF/pdb

• Classification: TRANSFERASE
• Organism(s): Neisseria meningitidis serogroup B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-11 Released: 2008-07-01 
• Deposition Author(s): Cochrane, F.C., Patchett, M.L., Jameson, G.B., Parker, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Re-Establishing a Metal-Binding Scaffold with Full Activity in the Metal-Independent Kdo8P Synthase from Neisseria Meningitidis

Cochrane, F.C., Patchett, M.L., Jameson, G.B., Parker, E.J.

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: 122.65 kDa 
• Atom Count: 8,466 
• Modeled Residue Count: 1,011 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase	A, B, C, D	280	Neisseria meningitidis serogroup B	Mutation(s): 0  Gene Names: kdsA EC: 2.5.1.55
UniProt
Find proteins for Q9JZ55 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JZ55  Go to UniProtKB:  Q9JZ55

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth C], J [auth C], K [auth C], N [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth B], F [auth C], G [auth C], L [auth D], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.515	α = 90
b = 85.295	β = 90
c = 162.686	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Cochrane, F.C., Patchett, M.L., Jameson, G.B., Parker, E.J.

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description