1V3Y | pdb_00001v3y

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), 0.216 (DCC)
R-Value Work:
0.171 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43522
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on 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), 0.216 (DCC)
R-Value Work: 0.171 (Depositor), 0.181 (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

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Entry History

Deposition Data

Released Date: 2004-12-28

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

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

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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.