4PWP | pdb_00004pwp

Crystal structure of DsbA from the Gram positive bacterium Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb4PWP/pdb

Classification: STRUCTURAL GENOMICS
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-21 Released: 2015-03-25
Deposition Author(s): Um, S.H., Kim, J.S., Jiao, L., Yoon, B.Y., Jo, I., Ha, N.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.204 (Depositor), 0.205 (DCC)
R-Value Work:
0.163 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4PWP

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

Literature

Crystal structure and biochemical characterization of DsbA from the Gram positive bacterium Corynebacterium diphtheriae

Um, S.H., Kim, J.S., Jiao, L., Yoon, B.Y., Jo, I., Ha, N.C.

To be published.

Macromolecule Content

Total Structure Weight: 27.14 kDa
Atom Count: 2,243
Modeled Residue Count: 250
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DsbA	A	250	Corynebacterium diphtheriae	Mutation(s): 0
UniProt
Find proteins for Q6NJK4 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NJK4 Go to UniProtKB: Q6NJK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NJK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.80 Å
R-Value Free: 0.204 (Depositor), 0.205 (DCC)
R-Value Work: 0.163 (Depositor), 0.167 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.819	α = 90
b = 68.435	β = 90
c = 69.139	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
Coot	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-03-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-25
Type: Initial release
Version 1.1: 2024-11-20
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.