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Yorodumi- PDB-1zbl: Bacillus halodurans RNase H catalytic domain mutant D192N in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zbl | ||||||
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Title | Bacillus halodurans RNase H catalytic domain mutant D192N in complex with 12-mer RNA/DNA hybrid | ||||||
Components |
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Keywords | HYDROLASE/RNA/DNA / RNase H / RNA/DNA hybrid / DDE motif / HYDROLASE-RNA-DNA COMPLEX | ||||||
Function / homology | Function and homology information ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nowotny, M. / Gaidamakov, S.A. / Crouch, R.J. / Yang, W. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2005 Title: Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis. Authors: Nowotny, M. / Gaidamakov, S.A. / Crouch, R.J. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zbl.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zbl.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zbl_validation.pdf.gz | 495.2 KB | Display | wwPDB validaton report |
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Full document | 1zbl_full_validation.pdf.gz | 505.3 KB | Display | |
Data in XML | 1zbl_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 1zbl_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zbl ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zbl | HTTPS FTP |
-Related structure data
Related structure data | 1zbfSC 1zbiC S: Starting model for refinement C: citing same article (ref.) |
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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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Number of models | 2 |
-Components
#1: RNA chain | Mass: 3772.296 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 3702.428 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 15986.051 Da / Num. of mol.: 2 / Fragment: catalytic domain (residues 59-196) / Mutation: D192N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS References: GenBank: 10173478, UniProt: Q9KEI9*PLUS, ribonuclease H #4: Chemical | ChemComp-MG / #5: 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: 2.3 Å3/Da / Density % sol: 46.2 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% ethanol, 0.35 M NaCl, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 18389 / Num. obs: 16268 / % possible obs: 88.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2 / Num. unique all: 1034 / % possible all: 56.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZBF Resolution: 2.2→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 323742.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.7368 Å2 / ksol: 0.354387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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