2YV2 | pdb_00002yv2

Crystal Structure of Succinyl-CoA Synthetase Alpha Chain from Aeropyrum pernix K1

PDB DOI: https://doi.org/10.2210/pdb2YV2/pdb

Classification: LIGASE
Organism(s): Aeropyrum pernix K1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-06 Released: 2007-10-09
Deposition Author(s): Niwa, H., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Succinyl-CoA Synthetase Alpha Chain from Aeropyrum pernix K1

Niwa, H., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 31.51 kDa
Atom Count: 2,184
Modeled Residue Count: 269
Deposited Residue Count: 297
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA synthetase alpha chain	A	297	Aeropyrum pernix K1	Mutation(s): 0 Gene Names: sucD EC: 6.2.1.5
UniProt
Find proteins for Q9YD40 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YD40 Go to UniProtKB: Q9YD40
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YD40
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.201 (Depositor), 0.201 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.542	α = 90
b = 137.183	β = 90
c = 74.867	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-09

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-10-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Refinement description

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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.