5GNP | pdb_00005gnp

Crystal structure of a Z-ring associated protein from Salmonella typhimurium

PDB DOI: https://doi.org/10.2210/pdb5GNP/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-07-22 Released: 2017-07-26
Deposition Author(s): Choi, H., Yoon, H.J., Lee, H.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.283 (Depositor), 0.280 (DCC)
R-Value Work:
0.251 (Depositor), 0.250 (DCC)
R-Value Observed:
0.253 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Z-ring associated protein from Salmonella typhimurium

Choi, H., Yoon, H.J., Lee, H.H.

To be published.

Macromolecule Content

Total Structure Weight: 28.29 kDa
Atom Count: 2,026
Modeled Residue Count: 245
Deposited Residue Count: 245
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein ZapD	A	245	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: zapD, STM0139
UniProt
Find proteins for P67693 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P67693 Go to UniProtKB: P67693
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P67693
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI 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]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.283 (Depositor), 0.280 (DCC)
R-Value Work: 0.251 (Depositor), 0.250 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.239	α = 90
b = 84.239	β = 90
c = 149.865	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-07-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-26
Type: Initial release
Version 1.1: 2017-11-15
Changes: Source and taxonomy
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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.