+Open data
-Basic information
Entry | Database: PDB / ID: 6mdw | ||||||
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Title | Mechanism of protease dependent DPC repair | ||||||
Components | SprT-like domain-containing protein Spartan | ||||||
Keywords | DNA BINDING PROTEIN / DPC repair protease | ||||||
Function / homology | Function and homology information protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / K63-linked polyubiquitin modification-dependent protein binding / protein autoprocessing / polyubiquitin modification-dependent protein binding / translesion synthesis / response to UV / ubiquitin binding / positive regulation of protein ubiquitination / Translesion Synthesis by POLH ...protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / K63-linked polyubiquitin modification-dependent protein binding / protein autoprocessing / polyubiquitin modification-dependent protein binding / translesion synthesis / response to UV / ubiquitin binding / positive regulation of protein ubiquitination / Translesion Synthesis by POLH / metalloendopeptidase activity / single-stranded DNA binding / double-stranded DNA binding / nuclear speck / DNA damage response / chromatin / proteolysis / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Li, F. / Raczynska, J. / Chen, Z. / Yu, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2019 Title: Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan. Authors: Li, F. / Raczynska, J.E. / Chen, Z. / Yu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mdw.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mdw.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 6mdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/6mdw ftp://data.pdbj.org/pub/pdb/validation_reports/md/6mdw | HTTPS FTP |
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-Related structure data
Related structure data | 6mdxSC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22712.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPRTN, C1orf124, DVC1, UNQ1880/PRO4323 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H040 |
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-Non-polymers , 5 types, 237 molecules
#2: Chemical | ChemComp-FLC / | ||
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#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-EDO / | ||
#5: Chemical | #6: 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: 2.1 Å3/Da / Density % sol: 42.63 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate tribasic dihydrate at pH 5.5, 14% (w/v) PEG8000, and 10 mM ATP |
-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 315r / Detector: CCD / Date: Oct 13, 2017 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 31618 / % possible obs: 99.4 % / Redundancy: 10.5 % / Biso Wilson estimate: 13.05 Å2 / Rpim(I) all: 0.024 / Net I/σ(I): 30.47 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1531 / Rpim(I) all: 0.253 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MDX Resolution: 1.5→32.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.55 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.442 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→32.58 Å
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Refine LS restraints |
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