6JF4

K1U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb6JF4/pdb

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

Deposited: 2019-02-08 Released: 2020-02-12
Deposition Author(s): Lee, I.H., Ho, T.H., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225
R-Value Work: 0.183
R-Value Observed: 0.185

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 structure of class I type b peptide deformylase from Acinetobacter baumannii

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

To be published.

Macromolecule Content

Total Structure Weight: 35.95 kDa
Atom Count: 2,397
Modelled Residue Count: 301
Deposited Residue Count: 318
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 [auth B], B [auth A]	159	Acinetobacter baumannii	Mutation(s): 0 Gene Names: def_1, def, def2, def_2, ABUW_2937, APD06_18825, BWP00_08140, C2U32_01090, CBI29_01007, DCD77_14985... def_1, def, def2, def_2, ABUW_2937, APD06_18825, BWP00_08140, C2U32_01090, CBI29_01007, DCD77_14985, DGS69_13130, DOL94_15075, SAMEA104305268_00677, SAMEA104305292_01437, SAMEA104305351_01290 EC: 3.5.1.88
UniProt
Find proteins for A0A098SKQ8 (Acinetobacter baumannii) Explore A0A098SKQ8 Go to UniProtKB: A0A098SKQ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A098SKQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K1U Query on K1U Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth A] MOL2 format, chain D [auth B] MOL2 format, chain F [auth A]	D [auth B], F [auth A]	(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 B] Focus chain F [auth A] Interactions & Density Focus chain D [auth B] Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain E [auth A]	C [auth B], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.967	α = 90
b = 77.351	β = 90
c = 96.582	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Lee, I.H.

Ho, T.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

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Help and Resources

6JF4

K1U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

K1U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

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)