6JF9 | pdb_00006jf9

Apo crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb6JF9/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa
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: 1.70 Å
R-Value Free:
0.281 (Depositor), 0.285 (DCC)
R-Value Work:
0.243 (Depositor), 0.253 (DCC)
R-Value Observed:
0.245 (Depositor)

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

Literature

Apo crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa

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

To be published.

Macromolecule Content

Total Structure Weight: 38.64 kDa
Atom Count: 2,591
Modeled Residue Count: 321
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	170	Pseudomonas aeruginosa	Mutation(s): 0 EC: 3.5.1.88
UniProt
Find proteins for A0A071LDC0 (Pseudomonas aeruginosa) Explore A0A071LDC0 Go to UniProtKB: A0A071LDC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A071LDC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.70 Å
R-Value Free: 0.281 (Depositor), 0.285 (DCC)
R-Value Work: 0.243 (Depositor), 0.253 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.486	α = 90
b = 122.045	β = 90
c = 149.38	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, 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.