2OM6 | pdb_00002om6

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 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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
• Version 1.3: 2024-11-13
  Changes: Structure summary