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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.193 (Depositor), 0.205 (DCC)
R-Value Work:
0.164 (Depositor), 0.202 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2DT4

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.21270
Primary Citation Related Structures:
2DT4

Organizational Affiliation

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58532
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.193 (Depositor), 0.205 (DCC)
R-Value Work: 0.164 (Depositor), 0.202 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-05-22

Deposition Author(s):

Revision History (Full details and data files)

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

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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.