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Yorodumi- PDB-1jxb: I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jxb | ||||||
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Title | I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI | ||||||
Components | Ribonuclease HI | ||||||
Keywords | HYDROLASE / MIXED ALPHA/BETA / 4-HELIX BUNDLE | ||||||
Function / homology | Function and homology information DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Spudich, G. / Lorenz, S. / Marqusee, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Propagation of a single destabilizing mutation throughout the Escherichia coli ribonuclease HI native state. Authors: Spudich, G. / Lorenz, S. / Marqusee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxb.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxb.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxb ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxb | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 17484.725 Da / Num. of mol.: 1 / Mutation: I53A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pSM101 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Y4, ribonuclease H |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.76 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 19, 1999 |
Radiation | Monochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. all: 207864 / Num. obs: 34997 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 91.4 |
Reflection | *PLUS Lowest resolution: 25 Å / Rmerge(I) obs: 0.062 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→12.5 Å
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Refinement step | Cycle: LAST / Resolution: 1.6→12.5 Å
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Refinement | *PLUS Highest resolution: 1.6 Å / % reflection Rfree: 11.07 % / Rfactor obs: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |