OCA Atlas for 1C0W

1C0W

Gene Regulation Dna

date

Jul 22, 1999

title

Crystal Structure Of The Cobalt-Activated Diphtheria Toxin R Dna Complex Reveals A Metal Binding Sh-Like Domain

authors

E.Pohl, R.K.Holmes, W.G.Hol

compound

source

Molecule: Dna (5'- D(Paptptpapgpgptptpapgpcpcptpapcpcpcptpa 3');
Chain: E
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Paptptpapgpgptptpapgpgpcptpapcpcpcptpa 3');
Chain: F
Engineered: Yes

Synthetic: Yes

Molecule: Diphtheria Toxin Repressor
Chain: A, B, C, D
Synonym: Iron-Dependent Diphtheria Tox Regulatory Element, Regulatory Factor;
Engineered: Yes

Organism_scientific: Corynebacterium Diphtheriae
Organism_taxid: 1717
Gene: Dtxr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5-Alpha

symmetry

Space Group: P 42 2 2

R_factor

0.249

R_Free

0.279

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
180.200	180.200	151.000	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.20 Å

ligand

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, D, C, B

Primary reference

Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain., Pohl E, Holmes RK, Hol WG, J Mol Biol 1999 Sep 24;292(3):653-67. PMID:10497029

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]

Biological Unit Coordinates (1c0w.pdb1.gz) 120 Kb

LPC: Ligand-Protein Contacts for 1C0W

CSU: Contacts of Structural Units for 1C0W

Likely Quarternary Molecular Structure file(s) for 1C0W

Structure Factors (330 Kb)

Retrieve 1C0W in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1C0W from S2C, [Save to disk]

Re-refined 1c0w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1C0W 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 1C0W

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 1C0W, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1c0wa3, region A:165-223 [Jmol] [rasmolscript] [script source]
- Domain d1c0wa1, region A:2-64 [Jmol] [rasmolscript] [script source]
- Domain d1c0wa2, region A:65-140 [Jmol] [rasmolscript] [script source]
- Domain d1c0wb3, region B:147-226 [Jmol] [rasmolscript] [script source]
- Domain d1c0wb1, region B:2-64 [Jmol] [rasmolscript] [script source]
- Domain d1c0wb2, region B:65-140 [Jmol] [rasmolscript] [script source]
- Domain d1c0wc3, region C:165-222 [Jmol] [rasmolscript] [script source]
- Domain d1c0wc1, region C:2-64 [Jmol] [rasmolscript] [script source]
- Domain d1c0wc2, region C:65-140 [Jmol] [rasmolscript] [script source]
- Domain d1c0wd3, region D:166-222 [Jmol] [rasmolscript] [script source]
- Domain d1c0wd1, region D:2-64 [Jmol] [rasmolscript] [script source]
- Domain d1c0wd2, region D:65-140 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1c0w_D] [1c0w_E] [1c0w_B] [1c0w_C] [1c0w_A] [1c0w] [1c0w_F]

SWISS-PROT database: [P33120]

Domain organization of [DTXR_CORDI] by SWISSPFAM

Domains found in 1C0W: [FeoA] [HTH_DTXR ] by SMART

Other resources with information on 1C0W

Community annotation for 1C0W 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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