1V3Y

The crystal structure of peptide deformylase from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1V3Y/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-11-07 Released: 2004-12-28 
• Deposition Author(s): Kamo, M., Kudo, N., Lee, W.C., Ito, K., Motoshim, H., Tanokura, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

The crystal structure of peptide deformylase from Thermus thermophilus HB8

Kamo, M., Kudo, N., Lee, W.C., Ito, K., Motoshim, H., Tanokura, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.34 kDa 
• Atom Count: 3,039 
• Modelled Residue Count: 337 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	192	Thermus thermophilus	Mutation(s): 1  EC: 3.5.1.88
UniProt
Find proteins for P43522 (Thermus thermophilus) Explore P43522  Go to UniProtKB:  P43522

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.582	α = 90
b = 62.582	β = 90
c = 105.271	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-28 
Deposition Author(s): Kamo, M., Kudo, N., Lee, W.C., Ito, K., Motoshim, H., Tanokura, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations