6CK7

Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin

PDB DOI: https://doi.org/10.2210/pdb6CK7/pdb

Classification: HYDROLASE/ANTIBIOTIC
Organism(s): Legionella pneumophila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-27 Released: 2018-03-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.208
R-Value Work: 0.182
R-Value Observed: 0.183

Starting Model: experimental
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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 a peptide deformylase from Legionella pneumophila bound to actinonin

Edwards, T.E., Horanyi, P.S., Lorimer, D.D.

To be published.

Macromolecule Content

Total Structure Weight: 83.44 kDa
Atom Count: 6,262
Modelled Residue Count: 688
Deposited Residue Count: 712
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, C, D	178	Legionella pneumophila	Mutation(s): 0 Gene Names: def_2, def, def_1, def_3, A1D14_13265, A9P85_13750, ERS240541_01674, ERS240560_02189, ERS253249_00325, lpymg_02824 EC: 3.5.1.88
UniProt
Find proteins for Q5ZSC4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSC4 Go to UniProtKB: Q5ZSC4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZSC4
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 F [auth A] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain I [auth B]	F [auth A], I [auth B], L [auth C], P [auth D]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	G [auth A], J [auth B], M [auth C], N [auth C], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.208
R-Value Work: 0.182
R-Value Observed: 0.183
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M36CK7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.65	α = 90
b = 132.06	β = 103.64
c = 90.38	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description