7YVY | pdb_00007yvy

Crystal structure of thiolase PFC_04095 from Pyrococcus furiosus

PDB DOI: https://doi.org/10.2210/pdb7YVY/pdb

Classification: TRANSFERASE
Organism(s): Pyrococcus furiosus COM1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-20 Released: 2023-09-06
Deposition Author(s): Singh, R., Das, A.K.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of thiolase PFC_04095 from Pyrococcus furiosus

Singh, R., Das, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 123.06 kDa
Atom Count: 7,760
Modeled Residue Count: 1,091
Deposited Residue Count: 1,164
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	A, B, C	388	Pyrococcus furiosus COM1	Mutation(s): 0 Gene Names: PFC_04095 EC: 2.3.1.9
UniProt
Find proteins for I6V154 (Pyrococcus furiosus COM1) Explore I6V154 Go to UniProtKB: I6V154
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6V154
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.252 (Depositor), 0.250 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.246	α = 90
b = 113.482	β = 123.03
c = 107.533	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR40990/MED/29/1540/2020

Revision History (Full details and data files)

Version 1.0: 2023-09-06
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, 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.