6JFG | pdb_00006jfg

K1U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb6JFG/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-02-08 Released: 2020-02-12
Deposition Author(s): Lee, I.H., Ho, T.H., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.265 (Depositor), 0.269 (DCC)
R-Value Work:
0.199 (Depositor), 0.203 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

K1U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus

Lee, I.H., Ho, T.H., Kang, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 20.99 kDa
Atom Count: 1,461
Modeled Residue Count: 183
Deposited Residue Count: 183
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	183	Staphylococcus aureus	Mutation(s): 0 Gene Names: def, def1, pdf1 EC: 3.5.1.88
UniProt
Find proteins for P68826 (Staphylococcus aureus) Explore P68826 Go to UniProtKB: P68826
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68826
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K1U (Subject of Investigation/LOI) Query on K1U Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid C₁₉ H₁₈ O₄ S XBDWLLDIBQGWMW-MRXNPFEDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.265 (Depositor), 0.269 (DCC)
R-Value Work: 0.199 (Depositor), 0.203 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.908	α = 90
b = 120.32	β = 90
c = 47.571	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-02-12
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.