6JET | pdb_00006jet

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

PDB DOI: https://doi.org/10.2210/pdb6JET/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: 2.60 Å
R-Value Free:
0.295 (Depositor), 0.292 (DCC)
R-Value Work:
0.247 (Depositor), 0.249 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 39.91 kDa
Atom Count: 2,651
Modeled Residue Count: 341
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	171	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
BB2 (Subject of Investigation/LOI) Query on BB2 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	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: 2.60 Å
R-Value Free: 0.295 (Depositor), 0.292 (DCC)
R-Value Work: 0.247 (Depositor), 0.249 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.666	α = 90
b = 112.903	β = 102.85
c = 43.678	γ = 90

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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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, Derived calculations, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.