3HPD | pdb_00003hpd

Structure of hydroxyethylthiazole kinase protein from pyrococcus horikoshii OT3

PDB DOI: https://doi.org/10.2210/pdb3HPD/pdb
Entry: 3HPD supersedes: 1V8A

Classification: TRANSFERASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-04 Released: 2009-06-16
Deposition Author(s): Jeyakanthan, J., Thamotharan, S., Kuramitsu, S., Yokoyama, S., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.184 (Depositor), 0.185 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3HPD

This is version 1.2 of the entry. See complete history.

Literature

Structure of Hydroxyethylthiazole Kinase Protein from Pyrococcus Horikoshii Ot3

Jeyakanthan, J., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 29.09 kDa
Atom Count: 2,159
Modeled Residue Count: 254
Deposited Residue Count: 265
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyethylthiazole kinase	A	265	Pyrococcus horikoshii OT3	Mutation(s): 0 EC: 2.7.1.50
UniProt
Find proteins for O58877 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58877 Go to UniProtKB: O58877
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58877
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.184 (Depositor), 0.185 (DCC)
R-Value Work: 0.164 (Depositor), 0.164 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.242	α = 90
b = 112.242	β = 90
c = 112.242	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Jeyakanthan, J.

Thamotharan, S.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

This entry supersedes: 1V8A

Revision History (Full details and data files)

Version 1.0: 2009-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.