2E3U | pdb_00002e3u

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.263 (Depositor), 0.221 (DCC)
R-Value Work:
0.228 (Depositor), 0.222 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.21381
Primary Citation Related Structures:
2E3U

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59282
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.263 (Depositor), 0.221 (DCC)
R-Value Work: 0.228 (Depositor), 0.222 (DCC)
R-Value Observed: 0.229 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2025-06-04
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.