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Yorodumi- PDB-7va2: PaOrn Oligoribonuclease D11A mutant with product GMP complex structure -
+Open data
-Basic information
Entry | Database: PDB / ID: 7va2 | |||||||||
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Title | PaOrn Oligoribonuclease D11A mutant with product GMP complex structure | |||||||||
Components | Oligoribonuclease | |||||||||
Keywords | HYDROLASE / PaOrn / Oligoribonuclease / Pseudomonas aeruginosa. | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Zhang, J. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: PaOrn Oligoribonuclease D11A mutant with product GMP complex structure Authors: Zhang, J. / Zhang, Q. / Bartlam, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7va2.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7va2.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 7va2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7va2_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7va2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7va2_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 7va2_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/7va2 ftp://data.pdbj.org/pub/pdb/validation_reports/va/7va2 | HTTPS FTP |
-Related structure data
Related structure data | 7v9zS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20809.586 Da / Num. of mol.: 2 / Mutation: D11A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: orn, PA4951 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P57665, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-IMD / | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-5GP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.94 Å3/Da / Density % sol: 68.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 1.2M (NH4)2HPO4, 0.1M imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 30350 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.05 Å2 / CC1/2: 0.969 / CC star: 0.992 / Rpim(I) all: 0.092 / Net I/σ(I): 15.61 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 1541 / CC1/2: 0.701 / CC star: 0.908 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7V9Z Resolution: 2.3→34.91 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7035 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→34.91 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 97.8144293403 Å / Origin y: 89.5912685673 Å / Origin z: 0.910304144951 Å
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Refinement TLS group | Selection details: all |