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Yorodumi- PDB-1y97: The human TREX2 3' exonuclease structure suggests a mechanism for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y97 | ||||||
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Title | The human TREX2 3' exonuclease structure suggests a mechanism for efficient non-processive DNA catalysis | ||||||
Components | Three prime repair exonuclease 2 | ||||||
Keywords | HYDROLASE / TREX2 / exonuclease | ||||||
Function / homology | Function and homology information double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 3'-5'-DNA exonuclease activity / DNA catabolic process / DNA metabolic process / molecular adaptor activity / DNA repair / magnesium ion binding / protein homodimerization activity / DNA binding ...double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 3'-5'-DNA exonuclease activity / DNA catabolic process / DNA metabolic process / molecular adaptor activity / DNA repair / magnesium ion binding / protein homodimerization activity / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Perrino, F.W. / Harvey, S. / McMillin, S. / Hollis, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: The Human TREX2 3' -> 5'-Exonuclease Structure Suggests a Mechanism for Efficient Nonprocessive DNA Catalysis. Authors: Perrino, F.W. / Harvey, S. / McMillin, S. / Hollis, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y97.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y97.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 1y97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y97_validation.pdf.gz | 412.5 KB | Display | wwPDB validaton report |
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Full document | 1y97_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 1y97_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1y97_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/1y97 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/1y97 | 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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Unit cell |
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Details | biological assembly is dimer in asymmetric unit |
-Components
#1: Protein | Mass: 26224.346 Da / Num. of mol.: 2 / Fragment: TREX2 exonuclease Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TREX2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQ50, exodeoxyribonuclease III #2: Water | ChemComp-HOH / | |
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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: 1.99 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.4 M ammonium phosphate, 7% PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97832, 0.97876, 0.9500 | ||||||||||||
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Mar 30, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.47→30 Å / Num. all: 14781 / Num. obs: 14344 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 19 | ||||||||||||
Reflection shell | Resolution: 2.47→2.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / Num. unique all: 1432 / Rsym value: 0.18 / % possible all: 80 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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LS refinement shell | Resolution: 2.5→2.61 Å
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