3KJJ

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

PDB DOI: https://doi.org/10.2210/pdb3KJJ/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.206
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Ren, J., Sainsbury, S., Owens, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 173.3 kDa
Atom Count: 11,793
Modelled Residue Count: 1,407
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NMB1025 protein	A, B, C, D, E 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 MC58)) Explore Q9JZJ4 Go to UniProtKB: Q9JZJ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JZJ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B]	M [auth A], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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: 1.90 Å
R-Value Free: 0.206
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.613	α = 90
b = 155.613	β = 90
c = 116.189	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Oxford Protein Production Facility (OPPF)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.