3EWM | pdb_00003ewm

Crystal structure of an uncharacterized sugar kinase PH1459 from pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb3EWM/pdb

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

Deposited: 2008-10-15 Released: 2008-11-18
Deposition Author(s): Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.189 (DCC)
R-Value Observed:
0.192 (Depositor)

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of an uncharacterized sugar kinase PH1459 from pyrococcus horikoshii

Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 69.53 kDa
Atom Count: 5,025
Modeled Residue Count: 595
Deposited Residue Count: 626
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized sugar kinase PH1459	A, B	313	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH1459, PHCC008 EC: 2.7.1
UniProt
Find proteins for O59128 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59128 Go to UniProtKB: O59128
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59128
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.239 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.189 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.757	α = 90
b = 79.373	β = 94.18
c = 82.99	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-18

Deposition Author(s):

Eswaramoorthy, S.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-11-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-12-27
Changes: Data collection, Database references
Version 1.4: 2024-11-13
Changes: 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.