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Yorodumi- PDB-7lwa: Human Exonuclease 5 crystal structure (T88E) in complex with ssDN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lwa | |||||||||
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Title | Human Exonuclease 5 crystal structure (T88E) in complex with ssDNA and Mg | |||||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE / HYDROLASE-DNA complex | |||||||||
Function / homology | Function and homology information single-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 3'-5' DNA exonuclease activity / interstrand cross-link repair / 4 iron, 4 sulfur cluster binding / Hydrolases; Acting on ester bonds / mitochondrion / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å | |||||||||
Authors | Tsai, C.L. / Tainer, J.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol.Cell / Year: 2021 Title: EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart. Authors: Hambarde, S. / Tsai, C.L. / Pandita, R.K. / Bacolla, A. / Maitra, A. / Charaka, V. / Hunt, C.R. / Kumar, R. / Limbo, O. / Le Meur, R. / Chazin, W.J. / Tsutakawa, S.E. / Russell, P. / ...Authors: Hambarde, S. / Tsai, C.L. / Pandita, R.K. / Bacolla, A. / Maitra, A. / Charaka, V. / Hunt, C.R. / Kumar, R. / Limbo, O. / Le Meur, R. / Chazin, W.J. / Tsutakawa, S.E. / Russell, P. / Schlacher, K. / Pandita, T.K. / Tainer, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lwa.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lwa.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/7lwa ftp://data.pdbj.org/pub/pdb/validation_reports/lw/7lwa | HTTPS FTP |
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-Related structure data
Related structure data | 7lw7SC 7lw8C 7lw9C 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
-Protein / DNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 38884.957 Da / Num. of mol.: 1 / Mutation: T61E, G145V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXO5, C1orf176, DEM1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H790, Hydrolases; Acting on ester bonds |
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#2: DNA chain | Mass: 3605.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 28 molecules
#3: Chemical | ChemComp-SF4 / |
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#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350 and 0.1 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.85→47.52 Å / Num. obs: 9998 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.992 / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.103 / Rrim(I) all: 0.377 / Net I/av σ(I): 8.1 / Net I/σ(I): 8.1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LW7 Resolution: 2.85→47.517 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.03 Å2 / Biso mean: 54.254 Å2 / Biso min: 24.44 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→47.517 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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