3B4Q

Crystal structure of a conserved protein domain (unknown function) from Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb3B4Q/pdb

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

Deposited: 2007-10-24 Released: 2007-11-06
Deposition Author(s): Tan, K., Maltseva, N., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.216
R-Value Work: 0.185
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The structure of a conserved protein domain (unknown function) from Corynebacterium diphtheriae.

Tan, K., Maltseva, N., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 20.01 kDa
Atom Count: 1,598
Modelled Residue Count: 177
Deposited Residue Count: 188
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 protein	A, B	94	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0 Gene Names: DIP0775
UniProt
Find proteins for Q6NIK0 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NIK0 Go to UniProtKB: Q6NIK0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NIK0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.216
R-Value Work: 0.185
R-Value Observed: 0.186
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.658	α = 90
b = 103.857	β = 90
c = 26.329	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

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 R01GM133198.