+Open data
-Basic information
Entry | Database: PDB / ID: 6oqm | ||||||
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Title | crystal structure of the MSH6 PWWP domain | ||||||
Components | DNA mismatch repair protein Msh6 | ||||||
Keywords | DNA BINDING PROTEIN / PWWP domain / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / positive regulation of helicase activity / meiotic mismatch repair / mismatched DNA binding / negative regulation of DNA recombination / isotype switching ...MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / positive regulation of helicase activity / meiotic mismatch repair / mismatched DNA binding / negative regulation of DNA recombination / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / ATP-dependent DNA damage sensor activity / somatic hypermutation of immunoglobulin genes / ATP-dependent activity, acting on DNA / mismatch repair / response to UV / methylated histone binding / intrinsic apoptotic signaling pathway / determination of adult lifespan / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / damaged DNA binding / intracellular membrane-bounded organelle / DNA repair / chromatin binding / chromatin / Golgi apparatus / enzyme binding / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Qin, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: crystal structure of the MSH6 PWWP domain Authors: Qin, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oqm.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oqm.ent.gz | 22.5 KB | Display | PDB format |
PDBx/mmJSON format | 6oqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oqm_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 6oqm_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 6oqm_validation.xml.gz | 6 KB | Display | |
Data in CIF | 6oqm_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/6oqm ftp://data.pdbj.org/pub/pdb/validation_reports/oq/6oqm | HTTPS FTP |
-Related structure data
Related structure data | 5vc8S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15145.189 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MSH6, GTBP / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V2R-pRARE2 / References: UniProt: P52701 | ||||||
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#2: Chemical | ChemComp-UNX / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-SO4 / #5: 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: 1.78 Å3/Da / Density % sol: 31.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.1 M sodium cacodylate pH 5.5, 0.01 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.2→47.09 Å / Num. obs: 5806 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.018 / Rrim(I) all: 0.059 / Net I/σ(I): 25.6 / Num. measured all: 61628 / Scaling rejects: 8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 5vc8 Resolution: 2.2→29.382 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0.27 / Phase error: 34.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.67 Å2 / Biso mean: 56.6048 Å2 / Biso min: 37.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→29.382 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %
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