OCA Atlas for 3BEP

3BEP

Transferase, Transcription Dna

date

Nov 19, 2007

title

Structure Of A Sliding Clamp On Dna

authors

R.E.Georgescu, S.S.Kim, O.Yurieva, J.Kuriyan, X.P.Kong, M.O'Donn

compound

source

Molecule: Dna (5'-D(Pdcpdcpdcpdapdtpdcpdgpdtpdapd
Chain: C
Engineered: Yes
Other_details: Dna Labeled At 5' End By Dye Cy5 (Labeled As Name 5cy). Only Half Of Dye Is Visible In Density;

Synthetic: Yes

Molecule: Dna (5'- D(Dtpdtpdtpdtpdapdtpdapdcpdgpdapdtpdgpdgpdg)-
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase III Subunit Beta
Chain: A, B
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Dnan
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

symmetry

Space Group: P 1

R_factor

0.210

R_Free

0.268

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
40.203	70.080	73.872	113.28	92.07	99.36

method

X-Ray Diffraction

resolution

1.92 Å

ligand

5CY

enzyme

Transferase E.C.2.7.7.7 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, B	3'-5' exonuclease activity

Primary reference

Structure of a sliding clamp on DNA., Georgescu RE, Kim SS, Yurieva O, Kuriyan J, Kong XP, O'Donnell M, Cell. 2008 Jan 11;132(1):43-54. PMID:18191219

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]

Biological Unit Coordinates (3bep.pdb1.gz) 134 Kb

LPC: Ligand-Protein Contacts for 3BEP

CSU: Contacts of Structural Units for 3BEP

Likely Quarternary Molecular Structure file(s) for 3BEP

Structure Factors (1014 Kb)

Retrieve 3BEP in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3BEP from S2C, [Save to disk]

Re-refined 3bep structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BEP 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 3BEP

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 3BEP, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3bep_B] [3bep_A] [3bep_D] [3bep_C] [3bep]

SWISS-PROT database: [P0A988]

Domain organization of [DPO3B_ECOLI] by SWISSPFAM

Domain found in 3BEP: [POL3Bc ] by SMART

Other resources with information on 3BEP

Community annotation for 3BEP 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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