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Yorodumi- PDB-1mc8: Crystal Structure of Flap Endonuclease-1 R42E mutant from Pyrococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mc8 | ||||||
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Title | Crystal Structure of Flap Endonuclease-1 R42E mutant from Pyrococcus horikoshii | ||||||
Components | Flap Endonuclease-1 | ||||||
Keywords | HYDROLASE / flexible loop | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Matsui, E. / Musti, K.V. / Abe, J. / Yamazaki, K. / Matsui, I. / Harata, K. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2002 Title: Molecular Structure and Novel DNA Binding Sites Located in Loops of Flap Endonuclease-1 from Pyrococcus horikoshii Authors: Matsui, E. / Musti, K.V. / Abe, J. / Yamazaki, K. / Matsui, I. / Harata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mc8.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mc8.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mc8_validation.pdf.gz | 433 KB | Display | wwPDB validaton report |
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Full document | 1mc8_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 1mc8_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 1mc8_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/1mc8 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/1mc8 | HTTPS FTP |
-Related structure data
Related structure data | 1a76S S: Starting model for refinement |
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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
#1: Protein | Mass: 38980.082 Da / Num. of mol.: 2 / Mutation: R42E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: O50123 |
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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: 2.63 Å3/Da / Density % sol: 53.17 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG6000, sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→34.7 Å / Num. all: 15903 / Num. obs: 15903 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.104 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.494 / % possible all: 98.6 |
Reflection | *PLUS % possible obs: 100 % / Num. measured all: 135478 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS Rmerge(I) obs: 0.494 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A76 Resolution: 3.1→8 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 37.8 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.15 Å
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Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 8 Å / Rfactor obs: 0.197 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.19 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.458 / Rfactor Rwork: 0.328 |