+Open data
-Basic information
Entry | Database: PDB / ID: 2etx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of MDC1 Tandem BRCT Domains | ||||||
Components | Mediator of DNA damage checkpoint protein 1 | ||||||
Keywords | CELL CYCLE / TANDEM BRCT DOMAINS HISTONE GAMMA-H2AX | ||||||
Function / homology | Function and homology information chromatin-protein adaptor activity / protein localization to site of double-strand break / DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...chromatin-protein adaptor activity / protein localization to site of double-strand break / DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromosome / Processing of DNA double-strand break ends / nuclear body / DNA repair / focal adhesion / DNA damage response / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.33 Å | ||||||
Authors | Wasielewski, E. / Kim, Y. / Joachimiak, A. / Thompson, J.R. / Mer, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Molecular Basis for the Association of Microcephalin (MCPH1) Protein with the Cell Division Cycle Protein 27 (Cdc27) Subunit of the Anaphase-promoting Complex. Authors: Singh, N. / Wiltshire, T.D. / Thompson, J.R. / Mer, G. / Couch, F.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2etx.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2etx.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 2etx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/2etx ftp://data.pdbj.org/pub/pdb/validation_reports/et/2etx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22913.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDC1 / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA (DE3) / References: UniProt: Q14676 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES 0.1M, PEG 8000 15%, ETHYLENE GLYCOL 15%, AMMONIUM ACETATE 0.2M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97954, 0.97967, 0.98120 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.33→36.84 Å / Num. all: 85639 / Num. obs: 85639 | ||||||||||||
Reflection shell | Resolution: 1.33→1.364 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.33→59.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 0.826 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.868 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→59.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.33→1.364 Å / Total num. of bins used: 20
|