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Yorodumi- PDB-2htf: The solution structure of the BRCT domain from human polymerase r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2htf | ||||||
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Title | The solution structure of the BRCT domain from human polymerase reveals homology with the TdT BRCT domain | ||||||
Components | DNA polymerase mu | ||||||
Keywords | TRANSFERASE / BRCT domain / alpha-beta-alpha sandwich | ||||||
Function / homology | Function and homology information Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Torsion angle dynamics, molecular dynamics refinement in explicit water solvent | ||||||
Model type details | minimized average | ||||||
Authors | DeRose, E.F. / Clarkson, M.W. / Gilmore, S.A. / Ramsden, D.A. / Mueller, G.A. / London, R.E. / Lee, A.L. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Solution structure of polymerase mu's BRCT Domain reveals an element essential for its role in nonhomologous end joining. Authors: DeRose, E.F. / Clarkson, M.W. / Gilmore, S.A. / Galban, C.J. / Tripathy, A. / Havener, J.M. / Mueller, G.A. / Ramsden, D.A. / London, R.E. / Lee, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2htf.cif.gz | 384 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2htf.ent.gz | 323.6 KB | Display | PDB format |
PDBx/mmJSON format | 2htf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2htf_validation.pdf.gz | 341.9 KB | Display | wwPDB validaton report |
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Full document | 2htf_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 2htf_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 2htf_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/2htf ftp://data.pdbj.org/pub/pdb/validation_reports/ht/2htf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11420.022 Da / Num. of mol.: 1 / Fragment: BRCT domain / Mutation: S20G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP87, DNA-directed DNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1mM polymerase mu BRCT domain, 25 mM d-Tris, 50 mM KCl, 0.02% NaN3, 5 mM DTT, pH 7.9, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM KCl / pH: 7.9 / Pressure: ambient / Temperature: 283 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Torsion angle dynamics, molecular dynamics refinement in explicit water solvent Software ordinal: 1 Details: The initial structures were computed using the auto noeassign feature of CYANA 2.1; 1503 NOE distance restraints were assigned, and 147 dihedral angle restraints were used in the calculation. ...Details: The initial structures were computed using the auto noeassign feature of CYANA 2.1; 1503 NOE distance restraints were assigned, and 147 dihedral angle restraints were used in the calculation. The 20 best CYANA structures were refined in explicit solvent using ARIA 2.0a with the 1506 NOE distance restraints, 147 dihedral angle restraints, 42 H-bond restraints, and 48 residual dipolar coupling restraints. | ||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 11 |