1VDK | pdb_00001vdk

Crystal structure of fumarase from thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb1VDK/pdb

Classification: LYASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-03-23 Released: 2004-04-13
Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.201 (Depositor), 0.190 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of fumarase from thermus thermophilus HB8

Mizutani, H., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 101.88 kDa
Atom Count: 7,680
Modeled Residue Count: 915
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate hydratase class II	A, B	466	Thermus thermophilus HB8	Mutation(s): 0 EC: 4.2.1.2
UniProt
Find proteins for P84127 (Thermus thermophilus) Explore P84127 Go to UniProtKB: P84127
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84127
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201 (Depositor), 0.190 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.336	α = 90
b = 140.122	β = 90
c = 135.372	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-04-13

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2004-04-13
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 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.