2R9I | pdb_00002r9i

Crystal structure of putative phage capsid protein domain from Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb2R9I/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Corynebacterium diphtheriae NCTC 13129
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-09-12 Released: 2007-12-18
Deposition Author(s): Wu, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.242 (Depositor), 0.261 (DCC)
R-Value Work:
0.219 (Depositor), 0.272 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2R9I

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of putative phage capsid protein domain from Corynebacterium diphtheriae.

Wu, R., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 15.52 kDa
Atom Count: 552
Modeled Residue Count: 72
Deposited Residue Count: 141
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phage capsid protein	A	141	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0 Gene Names: DIP0205
UniProt
Find proteins for Q6NK34 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NK34 Go to UniProtKB: Q6NK34
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NK34
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: 2.60 Å
R-Value Free: 0.242 (Depositor), 0.261 (DCC)
R-Value Work: 0.219 (Depositor), 0.272 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.905	α = 90
b = 102.905	β = 90
c = 102.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.