OCA Atlas for 1OTC

1OTC

Protein Dna

date

Nov 25, 1998

title

The O. Nova Telomere End Binding Protein Complexed With Sing Dna

authors

M.P.Horvath, V.L.Schweiker, J.M.Bevilacqua, J.A.Ruggles, S.C.Sch

compound

source

Molecule: Dna (5'-D(Gpgpgpgptptptptpgpgpgpg)-3'
Chain: D
Fragment: Single Strand Dodecamer Dna
Engineered: Yes

Synthetic: Yes

Molecule: Protein (Telomere-Binding Protein Alpha Subunit)
Chain: A
Synonym: Alpha Subunit
Engineered: Yes
Other_details: Alanine Version

Organism_scientific: Sterkiella Nova
Organism_taxid: 200597
Organelle: Macronucleous
Gene: Mac-56a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pkkt7-H
Expression_system_gene: Mac-56a

Molecule: Protein (Telomere-Binding Protein Beta Subunit)
Chain: B
Fragment: N-Terminal 28 Kda Core Domain
Synonym: Beta Subunit
Engineered: Yes
Other_details: Alanine Version

Organism_scientific: Sterkiella Nova
Organism_taxid: 200597
Organelle: Macronucleous
Gene: Mac-41a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Pkkt7-H
Expression_system_gene: Mac-41a

symmetry

Space Group: P 61 2 2

R_factor

0.251

R_Free

0.292

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
94.500	94.500	426.200	90.00	90.00	120.00

method

X-Ray Diffraction

resolution

2.80 Å

related structures

by homologous chain: 1KIX, 1PH1, 1PH7

Gene
Ontology

Chain	Function	Process	Component
A
B

Primary reference

Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA., Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA, Schultz SC, Cell 1998 Dec 23;95(7):963-74. PMID:9875850

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]

Biological Unit Coordinates (1otc.pdb1.gz) 113 Kb

CSU: Contacts of Structural Units for 1OTC

Likely Quarternary Molecular Structure file(s) for 1OTC

Structure Factors (387 Kb)

Retrieve 1OTC in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1OTC from S2C, [Save to disk]

Re-refined 1otc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1OTC in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1OTC

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1OTC, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1otca2, region A:205-328 [Jmol] [rasmolscript] [script source]
- Domain d1otca3, region A:329-495 [Jmol] [rasmolscript] [script source]
- Domain d1otca1, region A:37-204 [Jmol] [rasmolscript] [script source]
- Domain d1otcb_, region B [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1otc_D] [1otc] [1otc_A] [1otc_B]

SWISS-PROT database: [P29549] [P16458]

Domain organization of [TEBA_OXYNO] [TEBB_OXYNO] by SWISSPFAM

Domain found in 1OTC: [Telo_bind ] by SMART

Other resources with information on 1OTC

Community annotation for 1OTC at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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