6JEU | pdb_00006jeu

K1U bound crystal peptide deformylase from Acinetobacter baumanii

PDB DOI: https://doi.org/10.2210/pdb6JEU/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: 2.10 Å
R-Value Free:
0.280 (Depositor), 0.283 (DCC)
R-Value Work:
0.215 (Depositor), 0.222 (DCC)
R-Value Observed:
0.219 (Depositor)

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

K1U bound crystal peptide deformylase from Acinetobacter baumanii

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

To be published.

Macromolecule Content

Total Structure Weight: 39.63 kDa
Atom Count: 2,614
Modeled Residue Count: 340
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0VNL8
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 F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	(3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid C₁₉ H₁₈ O₄ S XBDWLLDIBQGWMW-MRXNPFEDSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.280 (Depositor), 0.283 (DCC)
R-Value Work: 0.215 (Depositor), 0.222 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.852	α = 90
b = 39.852	β = 90
c = 187.692	γ = 120

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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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Ho, T.H.

Lee, I.H.

Kang, L.W.

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, Derived calculations, Refinement description

6JEU | pdb_00006jeu

K1U bound crystal peptide deformylase from Acinetobacter baumanii

Literature

K1U bound crystal peptide deformylase from Acinetobacter baumanii

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)