1WPW | pdb_00001wpw

Crystal Structure of IPMDH from Sulfolobus tokodaii

PDB DOI: https://doi.org/10.2210/pdb1WPW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sulfurisphaera tokodaii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-09-14 Released: 2004-10-05
Deposition Author(s): Hirose, R., Sakurai, M., Suzuki, T., Moriyama, H., Sato, T., Yamagishi, A., Oshima, T., Tanaka, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.247 (Depositor), 0.191 (DCC)
R-Value Work:
0.190 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1WPW

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

Literature

Crystal Structure of IPMDH from Sulfolobus tokodaii

Hirose, R., Sakurai, M., Suzuki, T., Moriyama, H., Sato, T., Yamagishi, A., Oshima, T., Tanaka, N.

To be published.

Macromolecule Content

Total Structure Weight: 73.81 kDa
Atom Count: 5,265
Modeled Residue Count: 672
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A, B	336	Sulfurisphaera tokodaii	Mutation(s): 0 EC: 1.1.1.85
UniProt
Find proteins for P50455 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore P50455 Go to UniProtKB: P50455
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50455
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.247 (Depositor), 0.191 (DCC)
R-Value Work: 0.190 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.91	α = 90
b = 91.5	β = 90
c = 132.98	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-10-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Derived calculations, 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.