3KDQ | pdb_00003kdq

Crystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.

PDB DOI: https://doi.org/10.2210/pdb3KDQ/pdb

Classification: structural genomics, unknown function
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-10-23 Released: 2009-11-10
Deposition Author(s): Zhang, R., Wu, R., Tan, K., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.264 (Depositor), 0.259 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.

Zhang, R., Wu, R., Tan, K., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 72.15 kDa
Atom Count: 4,939
Modelled Residue Count: 609
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized conserved protein	A, B, C, D	154	Corynebacterium diphtheriae	Mutation(s): 0 Gene Names: Corynebacterium diphtheriae, DIP1984
UniProt
Find proteins for Q6NFB0 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NFB0 Go to UniProtKB: Q6NFB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NFB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.264 (Depositor), 0.259 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.676	α = 90
b = 132.484	β = 90
c = 176.314	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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.