6L4L | pdb_00006l4l

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of S. aureus CntK in inactive state

Ju, Y., Luo, S., Zhou, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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 EC: 5.1.1.24
UniProt
Find proteins for A0A0H3JU78 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JU78  Go to UniProtKB:  A0A0H3JU78

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Ju, Y., Luo, S., Zhou, H.

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

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary