2GKP | pdb_00002gkp

Protein of Unknown Function NMB0488 from Neisseria meningitidis

• PDB DOI: https://doi.org/10.2210/pdb2GKP/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-04-03 Released: 2006-05-02 
• Deposition Author(s): Osipiuk, J., Volkart, L., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.206 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

X-ray crystal structure of hypothetical protein NMB0488 from Neisseria meningitidis.

Osipiuk, J., Volkart, L., Bargassa, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.44 kDa 
• Atom Count: 1,847 
• Modeled Residue Count: 164 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein NMB0488	A	167	Neisseria meningitidis MC58	Mutation(s): 3  Gene Names: NMB0488
UniProt
Find proteins for Q9K0T5 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9K0T5  Go to UniProtKB:  Q9K0T5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.206 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.102	α = 90
b = 79.877	β = 90
c = 44.624	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-02 
Deposition Author(s): Osipiuk, J., Volkart, L., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-03-10
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Structure summary