2NVP | pdb_00002nvp

X-Ray Crystal Structure of Protein CPF_0428 from Clostridium perfringens. Northeast Structural Genomics Consortium Target CpR63.

PDB DOI: https://doi.org/10.2210/pdb2NVP/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Clostridium perfringens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-11-13 Released: 2006-11-28
Deposition Author(s): Forouhar, F., Chen, Y., Seetharaman, J., Cunningham, K., Ma, L.-C., Fang, Y., Baran, M.C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.245 (Depositor), 0.278 (DCC)
R-Value Work:
0.235 (Depositor), 0.247 (DCC)
R-Value Observed:
0.235 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the Hypothetical Protein CPF_0428 from Clostridium perfringens, Northeast Structural Genomics Target CpR63.

Forouhar, F., Chen, Y., Seetharaman, J., Cunningham, K., Ma, L.-C., Fang, Y., Baran, M.C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 51.33 kDa
Atom Count: 3,809
Modeled Residue Count: 430
Deposited Residue Count: 435
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A	435	Clostridium perfringens	Mutation(s): 10 Gene Names: CPF_0428
UniProt
Find proteins for Q8XNB2 (Clostridium perfringens (strain 13 / Type A)) Explore Q8XNB2 Go to UniProtKB: Q8XNB2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8XNB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.245 (Depositor), 0.278 (DCC)
R-Value Work: 0.235 (Depositor), 0.247 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.857	α = 90
b = 47.741	β = 96.03
c = 84.376	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-11-28

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-11-28
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Structure summary