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Yorodumi- PDB-6dp5: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dp5 | ||||||
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Title | Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 40 mM Mg2+ and 75 mM K+ for 40 s at 21 C | ||||||
Components |
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Keywords | HYDROLASE/DNA/RNA / protein-RNA-DNA complex / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / HYDROLASE-DNA-RNA 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.432 Å | ||||||
Authors | Samara, N.L. / Yang, W. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2018 Title: Cation trafficking propels RNA hydrolysis. Authors: Samara, N.L. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dp5.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dp5.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dp5_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6dp5_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6dp5_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 6dp5_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/6dp5 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/6dp5 | HTTPS FTP |
-Group deposition
ID | G_1001001 (54 entries) |
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Title | Cleavage of RNA by B. Halodurans Ribonuclease H1 |
Type | undefined |
Description | The structures represent different time points in the divalent and monovalent metal-dependent hydrolysis reaction of RNA by Ribonuclease H1, which is bound to an RNA/DNA hybrid in the crystal. |
-Related structure data
Related structure data | 1zblS 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 on special symmetry positions |
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-Components
-RNA chain , 2 types, 2 molecules Bb
#2: RNA chain | Mass: 1224.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / DNA chain , 2 types, 2 molecules AC
#1: Protein | Mass: 16330.462 Da / Num. of mol.: 1 / Fragment: Catalytic Domain residues 59-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: rnhA, BH0863 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KEI9, ribonuclease H |
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#4: DNA chain | Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 162 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-IOD / #8: Chemical | #9: Chemical | ChemComp-EDO / #10: 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: 2.45 Å3/Da / Density % sol: 49.72 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 14% PEG3350, 20% glycerol, 200 mM KI, and 25 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2018 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.43→20.01 Å / Num. obs: 32560 / % possible obs: 93.8 % / Redundancy: 1 % / Biso Wilson estimate: 19.2 Å2 / Net I/σ(I): 6.8 / Num. measured all: 32560 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: 1ZBL Resolution: 1.432→20.008 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.35 Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.23 Å2 / Biso mean: 29.2611 Å2 / Biso min: 13.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.432→20.008 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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