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Yorodumi- PDB-1avq: TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1avq | ||||||
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Title | TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS | ||||||
Components | LAMBDA EXONUCLEASEExodeoxyribonuclease (lambda-induced) | ||||||
Keywords | DEOXYRIBONUCLEASE / DNA RECOMBINATION AND REPAIR / 5'-3' EXONUCLEASE | ||||||
Function / homology | Function and homology information exodeoxyribonuclease (lambda-induced) / exonuclease activity / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage lambda (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR WITH ANOMALOUS DISPERSION / Resolution: 2.4 Å | ||||||
Authors | Kovall, R.A. / Matthews, B.W. | ||||||
Citation | Journal: Science / Year: 1997 Title: Toroidal structure of lambda-exonuclease. Authors: Kovall, R. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avq.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avq.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 1avq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avq ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avq | HTTPS FTP |
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-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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26165.809 Da / Num. of mol.: 3 / Mutation: 20 AMINO ACID N-TERMINAL HIS-TAG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Cell line: BL21 / Plasmid: PET-28(A+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS References: UniProt: P03697, exodeoxyribonuclease (lambda-induced) #2: Chemical | #3: Chemical | ChemComp-ACT / #4: 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: 4.8 Å3/Da / Density % sol: 74 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 4.7 Details: PROTEIN WAS CRYSTALLIZED FROM 1.2 M NH2SO4, 0.2 M NACL 0.1 M NAACETATE PH 4.7, AT 4 DEGREES CELSIUS., temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 62855 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.251 / % possible all: 94.3 |
Reflection | *PLUS Num. measured all: 291671 / Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: MIR WITH ANOMALOUS DISPERSION Resolution: 2.4→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: ANISOTROPIC SCALE FACTORS: B11 B22=7.26 B33=-14.53
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Solvent computation | Solvent model: TNT SOLVENT MODEL / Bsol: 235 Å2 / ksol: 0.922 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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