6L4L

Crystal structure of S. aureus CntK in inactive state

PDB DOI: https://doi.org/10.2210/pdb6L4L/pdb

Classification: ISOMERASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-18 Released: 2020-10-21
Deposition Author(s): Ju, Y., Luo, S., Zhou, H.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.231
R-Value Work: 0.201
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of S. aureus CntK in inactive state

Ju, Y., Luo, S., Zhou, H.

To be published.

Macromolecule Content

Total Structure Weight: 32.23 kDa
Atom Count: 2,076
Modelled Residue Count: 259
Deposited Residue Count: 281
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A	281	Staphylococcus aureus	Mutation(s): 0 Gene Names: dapF, cntK, DB727_02910, M1K003_1013
UniProt
Find proteins for A0A0H3JU78 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JU78 Go to UniProtKB: A0A0H3JU78
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3JU78
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.231
R-Value Work: 0.201
R-Value Observed: 0.202
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.748	α = 90
b = 60.293	β = 116.91
c = 76.991	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	81773636
National Science Foundation (China)	China	81803435

Revision History (Full details and data files)

Version 1.0: 2020-10-21
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.