3KJK | pdb_00003kjk

Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (monoclinic crystal form)

• PDB DOI: https://doi.org/10.2210/pdb3KJK/pdb

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


• Deposited: 2009-11-03 Released: 2009-11-24 
• Deposition Author(s): Ren, J., Sainsbury, S., Owens, R.J., Oxford Protein Production Facility (OPPF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.259 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis

Ren, J., Sainsbury, S., Owens, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 173.12 kDa 
• Atom Count: 11,385 
• Modeled Residue Count: 1,394 
• Deposited Residue Count: 1,536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NMB1025 protein	A, B, C, D, E, F, G, H, I, J, K, L	128	Neisseria meningitidis serogroup B	Mutation(s): 0  Gene Names: NMB1025
UniProt
Find proteins for Q9JZJ4 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JZJ4  Go to UniProtKB:  Q9JZJ4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.259 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.032	α = 90
b = 78.275	β = 103.62
c = 181.871	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Ren, J., Sainsbury, S., Owens, R.J., Oxford Protein Production Facility (OPPF)

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary