3BID

Crystal structure of the NMB1088 protein from Neisseria meningitidis. Northeast Structural Genomics Consortium target MR91

PDB DOI: https://doi.org/10.2210/pdb3BID/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Neisseria meningitidis MC58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-30 Released: 2007-12-18
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Mao, L., Fang, Y., Xiao, R., Owen, L.A., Maglaqui, M., Cunningham, K., Baran, M.C., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.290 (Depositor), 0.310 (DCC)
R-Value Work:
0.241 (Depositor), 0.260 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the NMB1088 protein from Neisseria meningitidis.

Forouhar, F., Neely, H., Seetharaman, J., Mao, L., Fang, Y., Xiao, R., Owen, L.A., Maglaqui, M., Cunningham, K., Baran, M.C., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 60.25 kDa
Atom Count: 3,787
Modelled Residue Count: 466
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0339 protein NMB1088	A, B, C, D, E A, B, C, D, E, F, G, H	64	Neisseria meningitidis MC58	Mutation(s): 0 Gene Names: NMB1088, 903505
UniProt
Find proteins for Q7DDI1 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q7DDI1 Go to UniProtKB: Q7DDI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7DDI1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.290 (Depositor), 0.310 (DCC)
R-Value Work: 0.241 (Depositor), 0.260 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.743	α = 89.39
b = 60.04	β = 90.81
c = 64.37	γ = 103.97

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2020-01-22
Changes: Database references, Derived calculations
Version 1.4: 2024-11-13
Changes: Data collection, Database references, Structure summary