2OM6

Hypothetical Protein (Probable Phosphoserine Phosph (PH0253) from Pyrococcus Horikoshii OT3

PDB DOI: https://doi.org/10.2210/pdb2OM6/pdb

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

Deposited: 2007-01-21 Released: 2008-01-29
Deposition Author(s): Jeyakanthan, J., Vaijayanthimala, S., Gayathri, D., Velmurugan, D., Baba, S., Ebihara, A., Shinkai, A., Kuramitsu, S., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.259
R-Value Work: 0.186
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

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

Literature

Hypothetical Protein (Probable Phosphoserine Phosph (PH0253) from Pyrococcus Horikoshii OT3

Jeyakanthan, J., Vaijayanthimala, S., Gayathri, D., Velmurugan, D., Baba, S., Ebihara, A., Shinkai, A., Kuramitsu, S., Shiro, Y., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 54.81 kDa
Atom Count: 4,207
Modelled Residue Count: 466
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable phosphoserine phosphatase	A, B	235	Pyrococcus horikoshii OT3	Mutation(s): 0 EC: 3.1.3.3
UniProt
Find proteins for O57991 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57991 Go to UniProtKB: O57991
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O57991
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

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: 2.20 Å
R-Value Free: 0.259
R-Value Work: 0.186
R-Value Observed: 0.186
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.052	α = 90
b = 66.239	β = 107.62
c = 79.014	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-01-29

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-01-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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Help and Resources

2OM6

Hypothetical Protein (Probable Phosphoserine Phosph (PH0253) from Pyrococcus Horikoshii OT3

Hypothetical Protein (Probable Phosphoserine Phosph (PH0253) from Pyrococcus Horikoshii OT3

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)