6JF6 | pdb_00006jf6

Met-ala-ser bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb6JF6/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.292 (Depositor), 0.298 (DCC)
R-Value Work:
0.210 (Depositor), 0.215 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Met-ala-ser bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

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

To be published.

Macromolecule Content

Total Structure Weight: 71.63 kDa
Atom Count: 4,961
Modeled Residue Count: 634
Deposited Residue Count: 643
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C, D	160	Acinetobacter baumannii	Mutation(s): 0 Gene Names: def, C3415_07350, IX87_00730 EC: 3.5.1.88

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MET-ALA-SER	E	3	synthetic construct	Mutation(s): 0

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 I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], H [auth C], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.292 (Depositor), 0.298 (DCC)
R-Value Work: 0.210 (Depositor), 0.215 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.37	α = 90
b = 39.347	β = 89.98
c = 110.353	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.