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Yorodumi- PDB-7p4r: Ultra High Resolution X-ray Structure of Orthorhombic Bovine Panc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p4r | |||||||||
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Title | Ultra High Resolution X-ray Structure of Orthorhombic Bovine Pancreatic Ribonuclease at 100K | |||||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | |||||||||
Keywords | HYDROLASE / Nucleic acid / RNA / multiple conformations / water structure | |||||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å | |||||||||
Authors | Lisgarten, D.R. / Palmer, R.A. / Cooper, J.B. / Naylor, C.E. / Howlin, B.J. / Lisgarten, J.N. / Najmudin, S. / Lobley, C.M.C. | |||||||||
Citation | Journal: BMC Chem / Year: 2023 Title: Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K. Authors: Lisgarten, D.R. / Palmer, R.A. / Cooper, J.B. / Naylor, C.E. / Talbert, R.C. / Howlin, B.J. / Lisgarten, J.N. / Konc, J. / Najmudin, S. / Lobley, C.M.C. #1: Journal: Acta Crystallogr A / Year: 1989 Title: Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model. Authors: Howlin, B. / Moss, D.S. / Harris, G.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p4r.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p4r.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/7p4r ftp://data.pdbj.org/pub/pdb/validation_reports/p4/7p4r | HTTPS FTP |
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-Related structure data
Related structure data | 3rn3S 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: 13708.326 Da / Num. of mol.: 1 / Mutation: None Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Organ: Pancreas / Production host: Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease | ||||||
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#2: Chemical | ChemComp-EOH / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.3 % Description: The Ribonuclease A crystals were long needles of the order of 0.5 mm long by about 0.05 mm by 0.05 mm. |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 7 Details: 100mg of powdered Ribonuclease A in 1ml of distilled water dissolved in 2ml of ice cold absolute ethanol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.77 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→51.89 Å / Num. obs: 87934 / % possible obs: 95.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 0.85→0.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2925 / Rpim(I) all: 0.55 / Rrim(I) all: 0.893 / % possible all: 65.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3rn3 Resolution: 0.85→34.294 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.122 / WRfactor Rwork: 0.106 / SU B: 0.399 / SU ML: 0.011 / Average fsc free: 0.9674 / Average fsc work: 0.9705 / Cross valid method: FREE R-VALUE / ESU R: 0.015 / ESU R Free: 0.016 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.596 Å2
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Refinement step | Cycle: LAST / Resolution: 0.85→34.294 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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