2DT4 | pdb_00002dt4

Crystal structure of Pyrococcus horikoshii a plant- and prokaryote-conserved (PPC) protein at 1.60 resolution

• PDB DOI: https://doi.org/10.2210/pdb2DT4/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-07-10 Released: 2007-05-22 
• Deposition Author(s): Lin, L., Nakano, H., Uchiyama, S., Fujimoto, S., Matsunaga, S., Nakamura, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.193 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 A resolution

Lin, L., Nakano, H., Nakamura, S., Uchiyama, S., Fujimoto, S., Matsunaga, S., Kobayashi, Y., Ohkubo, T., Fukui, K.

(2007) Proteins 67: 505-507

• PubMed: 17295322 
• DOI: https://doi.org/10.1002/prot.21270
• Primary Citation of Related Structures:  
  2DT4

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Organizational Affiliation: 

Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871 Osaka, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.21 kDa 
• Atom Count: 1,317 
• Modeled Residue Count: 143 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH0802	A	143	Pyrococcus horikoshii	Mutation(s): 0
UniProt
Find proteins for O58532 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58532  Go to UniProtKB:  O58532

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.193 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.922	α = 90
b = 53.922	β = 90
c = 159.181	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Lin, L., Nakano, H., Uchiyama, S., Fujimoto, S., Matsunaga, S., Nakamura, S.

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations