3D7A

Crystal structure of DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb3D7A/pdb

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


• Deposited: 2008-05-20 Released: 2008-12-09 
• Deposition Author(s): Shirokane, M., Miyazono, K.I., Sawano, Y., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.281 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3.

Miyazono, K.I., Shirokane, M., Sawano, Y., Tanokura, M.

(2008) Proteins 74: 256-260

• PubMed: 18831045 
• DOI: https://doi.org/10.1002/prot.22255
• Primary Citation of Related Structures:  
  3D7A

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Organizational Affiliation: 

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 32.16 kDa 
• Atom Count: 2,393 
• Modelled Residue Count: 271 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0201 protein PH1010	A, B	138	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1010
UniProt
Find proteins for O58738 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58738  Go to UniProtKB:  O58738

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.281 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.934	α = 90
b = 49.526	β = 90
c = 132.695	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Shirokane, M., Miyazono, K.I., Sawano, Y., Tanokura, M.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2024-03-20
  Changes: Advisory, Data collection, Database references