1WS0 | pdb_00001ws0

Structure analysis of peptide deformylase from Bacillus cereus

PDB DOI: https://doi.org/10.2210/pdb1WS0/pdb

Classification: HYDROLASE
Organism(s): Bacillus cereus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-10-29 Released: 2005-09-13
Deposition Author(s): Moon, J.H., Park, J.K., Kim, E.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.223 (Depositor), 0.221 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1WS0

This is version 1.3 of the entry. See complete history.

Literature

Structure analysis of peptide deformylase from Bacillus cereus

Moon, J.H., Park, J.K., Kim, E.E.

(2005) Proteins 61: 217-220

PubMed: 16049914 Search on PubMed
DOI: https://doi.org/10.1002/prot.20526
Primary Citation Related Structures:
1WS0, 1WS1

Organizational Affiliation

Biomedical Research Center, Life Sciences Division, Korea Institute of Science and Technology, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 17.56 kDa
Atom Count: 1,303
Modeled Residue Count: 151
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide deformylase 1	A	156	Bacillus cereus	Mutation(s): 0 Gene Names: DEF1 EC: 3.5.1.88
UniProt
Find proteins for Q819U0 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q819U0 Go to UniProtKB: Q819U0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q819U0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.223 (Depositor), 0.221 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.33	α = 90
b = 42.802	β = 90
c = 84.806	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-09-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-09-13
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.