2E3U

Crystal structure analysis of Dim2p from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2E3U/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-29 Released: 2007-10-23 
• Deposition Author(s): Tanokura, M., Jia, M.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Starting Model: experimental

Literature

Crystal structure of Dim2p: a preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 A

Jia, M.Z., Ohtsuka, J., Lee, W.C., Nagata, K., Tanokura, M.

(2007) Proteins 69: 428-432

• PubMed: 17654551 
• DOI: https://doi.org/10.1002/prot.21381
• Primary Citation of Related Structures:  
  2E3U

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Organizational Affiliation: 

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.19 kDa 
• Atom Count: 1,340 
• Modelled Residue Count: 166 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH1566	A	219	Pyrococcus horikoshii OT3	Mutation(s): 0
UniProt
Find proteins for O59282 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59282  Go to UniProtKB:  O59282

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.949	α = 90
b = 47.45	β = 90
c = 95.722	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Tanokura, M., Jia, M.Z.

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Refinement description