6JER | pdb_00006jer

Apo crystal structure of class I type a peptide deformylase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb6JER/pdb

Classification: HYDROLASE
Organism(s): Acinetobacter baumannii MRSN 3527
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-02-07 Released: 2020-02-12
Deposition Author(s): Ho, T.H., Lee, I.H., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.289 (Depositor), 0.290 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Expression, crystallization, and preliminary X-ray crystallographic analysis of peptide deformylase from Acinetobacter baumanii

(2017) Korean Soc Struct Biology 5: 49-52

Macromolecule Content

Total Structure Weight: 39 kDa
Atom Count: 2,723
Modeled Residue Count: 340
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	170	Acinetobacter baumannii MRSN 3527	Mutation(s): 0 Gene Names: def_1, def, T630_0214 EC: 3.5.1.88
UniProt
Find proteins for B0VNL8 (Acinetobacter baumannii (strain SDF)) Explore B0VNL8 Go to UniProtKB: B0VNL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0VNL8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.289 (Depositor), 0.290 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.425	α = 90
b = 39.425	β = 90
c = 187.888	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

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

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.