2YZQ | pdb_00002yzq

Crystal structure of uncharacterized conserved protein from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb2YZQ/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-06 Released: 2007-11-06 
• Deposition Author(s): Kanagawa, M., Minami, Y., Watanabe, N., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystal structure of uncharacterized conserved protein from Pyrococcus horikoshii

Kanagawa, M., Minami, Y., Watanabe, N., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.35 kDa 
• Atom Count: 2,133 
• Modeled Residue Count: 224 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH1780	A	282	Pyrococcus horikoshii	Mutation(s): 0
UniProt
Find proteins for O59416 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59416  Go to UniProtKB:  O59416

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.753	α = 90
b = 75.008	β = 119.53
c = 49.661	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Kanagawa, M., Minami, Y., Watanabe, N., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations