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Yorodumi- PDB-4j6a: Crystal structure of Ribonuclease A soaked in 40% 2,2,2-Trifluoro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j6a | ||||||
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Title | Crystal structure of Ribonuclease A soaked in 40% 2,2,2-Trifluoroethanol: One of twelve in MSCS set | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / Endoribonuclease | ||||||
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 / molecular replacement / Resolution: 2.04 Å | ||||||
Authors | Kearney, B.M. / Dechene, M. / Swartz, P.D. / Mattos, C. | ||||||
Citation | Journal: to be published Title: DRoP: A program for analysis of water structure on protein surfaces Authors: Kearney, B.M. / Roberts, D. / Dechene, M. / Swartz, P.D. / Mattos, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j6a.cif.gz | 39.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j6a.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j6a_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 4j6a_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 4j6a_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 4j6a_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/4j6a ftp://data.pdbj.org/pub/pdb/validation_reports/j6/4j6a | HTTPS FTP |
-Related structure data
Related structure data | 4j5zC 4j60C 4j61C 4j62C 4j63C 4j64C 4j65C 4j66C 4j67C 4j68C 4j69C 1rphS C: citing same article (ref.) 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
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: 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: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 35% ammonium sulfate, 1.5 M sodium chloride, 35 mg/mL protein in 20 mM sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2004 / Details: mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→50 Å / Num. all: 9877 / Num. obs: 9877 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rmerge(I) obs: 0.125 / Χ2: 1.093 / Net I/σ(I): 6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RPH Resolution: 2.04→41.713 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 19.61 / Stereochemistry target values: ML
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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 max: 67.87 Å2 / Biso mean: 26.0221 Å2 / Biso min: 10.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→41.713 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: 7 / % reflection obs: 100 %
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