+Open data
-Basic information
Entry | Database: PDB / ID: 1j74 | ||||||
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Title | Crystal Structure of Mms2 | ||||||
Components | MMS2 | ||||||
Keywords | UNKNOWN FUNCTION / Mms2 / Uev / Ubiquitin / Ubc / DNA repair | ||||||
Function / homology | Function and homology information error-free postreplication DNA repair / UBC13-MMS2 complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...error-free postreplication DNA repair / UBC13-MMS2 complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Formation of Incision Complex in GG-NER / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / protein ubiquitination / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Moraes, T.F. / Edwards, R.A. / McKenna, S. / Pastushok, L. / Xiao, W. / Glover, J.N.M. / Ellison, M.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13. Authors: Moraes, T.F. / Edwards, R.A. / McKenna, S. / Pastushok, L. / Xiao, W. / Glover, J.N. / Ellison, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j74.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j74.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j74_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 1j74_full_validation.pdf.gz | 426.3 KB | Display | |
Data in XML | 1j74_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 1j74_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j74 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j74 | HTTPS FTP |
-Related structure data
Related structure data | 1j7dSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16380.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15819 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 6000, 25mM NaCl, 100mM citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-24 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 21, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 9995 / Num. obs: 9973 / % possible obs: 97.9 % / Redundancy: 5.35 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 4.5 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 20 / Num. unique all: 445 / Rsym value: 12.9 / % possible all: 87.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 53554 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1J7D Resolution: 1.9→20 Å / Stereochemistry target values: CNS template
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.98 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.213 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |