+Open data
-Basic information
Entry | Database: PDB / ID: 7lw8 | |||||||||
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Title | Human Exonuclease 5 crystal structure in complex with a ssDNA | |||||||||
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 / 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: 2.88 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 | 7lw8.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lw8.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 7lw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/7lw8 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/7lw8 | HTTPS FTP |
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-Related structure data
Related structure data | 7lw7SC 7lw9C 7lwaC 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: 38856.949 Da / Num. of mol.: 1 / Mutation: 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, 45 molecules
#3: Chemical | ChemComp-SF4 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-IMD / | #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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350 and 0.2 M lithium acetate |
-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: Mar 13, 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: 2.88→48.18 Å / Num. obs: 9904 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.436 / Rpim(I) all: 0.126 / Rrim(I) all: 0.455 / Net I/av σ(I): 6.4 / Net I/σ(I): 6.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LW7 Resolution: 2.88→48.178 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.58 / 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: 110.26 Å2 / Biso mean: 39.7004 Å2 / Biso min: 9.64 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.88→48.178 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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