+Open data
-Basic information
Entry | Database: PDB / ID: 3asm | ||||||
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Title | Crystal structure of Q54A mutant protein of Bst-RNase HIII | ||||||
Components | Ribonuclease HIII | ||||||
Keywords | HYDROLASE / RNase / DNA/RNA binding | ||||||
Function / homology | Function and homology information ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / mismatch repair / RNA-DNA hybrid ribonuclease activity / magnesium ion binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å | ||||||
Authors | Angkawidjaja, C. / Kanaya, S. | ||||||
Citation | Journal: Febs Lett. / Year: 2011 Title: Identification of the substrate binding site in the N-terminal TBP-like domain of RNase H3. Authors: Miyashita, S. / Tadokoro, T. / Angkawidjaja, C. / You, D.-J. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3asm.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3asm.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 3asm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3asm_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 3asm_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 3asm_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3asm_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/3asm ftp://data.pdbj.org/pub/pdb/validation_reports/as/3asm | HTTPS FTP |
-Related structure data
Related structure data | 2d0aS 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: 33815.895 Da / Num. of mol.: 1 / Mutation: Q54A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pET25b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Mic2067(de3) / References: UniProt: Q6L6Q4, 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: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.085M Tris-HCl pH 8.5, 0.17M lithium sulfate, 25.5% PEG 4000, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 14, 2008 / Details: mirrors |
Radiation | Monochromator: mirros / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 11445 / % possible obs: 99.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Rsym value: 0.086 / Net I/σ(I): 18.5 / Num. measured all: 240534 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.33 / Num. unique all: 1102 / Rsym value: 0.355 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D0A Resolution: 2.603→44.19 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.81 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R Free: 0.29 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.873 Å2
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Refinement step | Cycle: LAST / Resolution: 2.603→44.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.603→2.67 Å / Total num. of bins used: 20
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