1WS1

Structure analysis of peptide deformylase from Bacillus cereus

• PDB DOI: https://doi.org/10.2210/pdb1WS1/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.184 
• R-Value Observed: 0.223 

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 
• DOI: https://doi.org/10.1002/prot.20526
• Primary Citation of Related Structures:  
  1WS0, 1WS1

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.95 kDa 
• Atom Count: 1,310 
• Modelled Residue Count: 151 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	C [auth A]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BB2	PDBBind:  1WS1	Ki: 0.28 (nM) from 1 assay(s)
	Binding MOAD:  1WS1	Ki: 0.28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.184 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.31	α = 90
b = 44.558	β = 90
c = 84.474	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-13 
Deposition Author(s): Moon, J.H., Park, J.K., Kim, E.E.

Revision History  

• 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