3OI8 | pdb_00003oi8

The crystal structure of functionally unknown conserved protein domain from Neisseria meningitidis MC58

• PDB DOI: https://doi.org/10.2210/pdb3OI8/pdb

• Classification: Structural genomics, Unknown function
• Organism(s): Neisseria meningitidis serogroup B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-18 Released: 2010-09-22 
• Deposition Author(s): Zhang, R., Tan, K., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.232 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

The crystal structure of functionally unknown conserved protein domain from Neisseria meningitidis MC58

Zhang, R., Tan, K., Li, H., Cobb, G., Joachimiak, A.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 36.81 kDa 
• Atom Count: 2,689 
• Modeled Residue Count: 310 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	156	Neisseria meningitidis serogroup B	Mutation(s): 0  Gene Names: NMB0537
UniProt
Find proteins for Q9K0P8 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9K0P8  Go to UniProtKB:  Q9K0P8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	C [auth A], F [auth B]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.232 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.64	α = 90
b = 52.156	β = 112.67
c = 64.01	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Zhang, R., Tan, K., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary