7DMS

A Fe(II)-binding effector of Yersinia pseudotuberculosis

PDB DOI: https://doi.org/10.2210/pdb7DMS/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Yersinia pseudotuberculosis IP 32953
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-07 Released: 2021-12-08
Deposition Author(s): Ouyang, S., Hongxin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.267
R-Value Work: 0.203
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A Fe(II)-binding effector of Yersinia pseudotuberculosis

Ouyang, S., Hongxin, G.

To be published.

Macromolecule Content

Total Structure Weight: 11.05 kDa
Atom Count: 869
Modelled Residue Count: 94
Deposited Residue Count: 94
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe(II)-binding effector	A	94	Yersinia pseudotuberculosis IP 32953	Mutation(s): 0 Gene Names: YPTB3614
UniProt
Find proteins for Q665A4 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q665A4 Go to UniProtKB: Q665A4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q665A4
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: 1.96 Å
R-Value Free: 0.267
R-Value Work: 0.203
R-Value Observed: 0.206
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.904	α = 90
b = 47.465	β = 90
c = 67.638	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-12-08
Type: Initial release

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.