1IX1

Crystal Structure of P.aeruginosa Peptide deformylase Complexed with Antibiotic Actinonin

PDB DOI: https://doi.org/10.2210/pdb1IX1/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-06-07 Released: 2003-09-09
Deposition Author(s): Kim, H.-W., Yoon, H.-J., Lee, J.Y., Han, B.W., Yang, J.K., Lee, B.I., Ahn, H.J., Lee, H.H., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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 of Related Structures:
1IX1, 1Q1Y

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 40.89 kDa
Atom Count: 3,106
Modelled Residue Count: 338
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide deformylase	A, B	171	Pseudomonas aeruginosa	Mutation(s): 0 EC: 3.5.1.88
UniProt
Find proteins for Q9I7A8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I7A8 Go to UniProtKB: Q9I7A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I7A8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BB2 Query on BB2 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MHA Query on MHA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID C₆ H₁₀ N₂ O₅ QZTKDVCDBIDYMD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.75	α = 90
b = 74.46	β = 90
c = 77.18	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-09-09
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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1IX1

Crystal Structure of P.aeruginosa Peptide deformylase Complexed with Antibiotic Actinonin

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)