3KXA | pdb_00003kxa

Crystal Structure of NGO0477 from Neisseria gonorrhoeae

• PDB DOI: https://doi.org/10.2210/pdb3KXA/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Neisseria gonorrhoeae FA 1090
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-02 Released: 2010-01-19 
• Deposition Author(s): Ren, J., Sainsbury, S., Nettleship, J.E., Owens, R.J., Oxford Protein Production Facility (OPPF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.280 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

The crystal structure of NGO0477 from Neisseria gonorrhoeae reveals a novel protein fold incorporating a helix-turn-helix motif.

Ren, J., Sainsbury, S., Nettleship, J.E., Saunders, N.J., Owens, R.J.

(2010) Proteins 78: 1798-1802

• PubMed: 20196080 
• DOI: https://doi.org/10.1002/prot.22698
• Primary Citation Related Structures: 
  3KXA

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Organizational Affiliation: 
• The Oxford Protein Production Facility and Division of Structural Biology, University of Oxford, Oxford OX3 7BN, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.97 kDa 
• Atom Count: 4,160 
• Modeled Residue Count: 522 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D	141	Neisseria gonorrhoeae FA 1090	Mutation(s): 0  Gene Names: NGO0477
UniProt
Find proteins for Q5F9C2 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F9C2  Go to UniProtKB:  Q5F9C2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASN	E [auth A], QA [auth D], V [auth B], Y [auth C]	ASPARAGINE C4 H8 N2 O3 DCXYFEDJOCDNAF-REOHCLBHSA-N
CL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], W [auth B], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], Z [auth C]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.280 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.823	α = 90
b = 124.823	β = 90
c = 137.577	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Ren, J., Sainsbury, S., Nettleship, J.E., Owens, R.J., Oxford Protein Production Facility (OPPF)

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary