3FWX | pdb_00003fwx

The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor str. N16961

PDB DOI: https://doi.org/10.2210/pdb3FWX/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-19 Released: 2009-03-17
Deposition Author(s): Zhang, R., Zhou, M., Stam, J., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.262 (Depositor), 0.272 (DCC)
R-Value Work:
0.202 (Depositor), 0.217 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor

Zhang, R., Zhou, M., Stam, J., Anderson, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 38.85 kDa
Atom Count: 2,911
Modeled Residue Count: 330
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	169	Vibrio cholerae O395	Mutation(s): 0 Gene Names: def-1, GI:15640078, VC0395_A2473 EC: 3.5.1.88
UniProt
Find proteins for Q9KVU3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVU3 Go to UniProtKB: Q9KVU3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KVU3
Sequence Annotations Expand
Reference Sequence

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 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]	ZINC ION Zn PTFCDOFLOPIGGS-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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.262 (Depositor), 0.272 (DCC)
R-Value Work: 0.202 (Depositor), 0.217 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.305	α = 90
b = 61.456	β = 90
c = 210.343	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.