1Q1Y | pdb_00001q1y

Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin

PDB DOI: https://doi.org/10.2210/pdb1Q1Y/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-07-23 Released: 2004-07-23
Deposition Author(s): Yoon, H.J., Lee, S.K., Kim, H.L., Kim, H.W., Kim, H.W., Lee, J.Y., Mikami, B., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.205 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent

Yoon, H.J., Kim, H.L., Lee, S.K., Kim, H.W., Kim, H.W., Lee, J.Y., Mikami, B., Suh, S.W.

(2004) Proteins 57: 639-642

PubMed: 15382235 Search on PubMed
DOI: https://doi.org/10.1002/prot.20231
Primary Citation Related Structures:
1IX1, 1Q1Y

Organizational Affiliation

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 22.14 kDa
Atom Count: 1,749
Modeled Residue Count: 186
Deposited Residue Count: 191
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	191	Staphylococcus aureus	Mutation(s): 1 Gene Names: SA1100 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
BB2 Query on BB2 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]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.235 (Depositor), 0.235 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.417	α = 90
b = 120.844	β = 90
c = 48.057	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-07-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-23
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-02-08
Changes: Other, Version format compliance
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary