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Yorodumi- PDB-1ymw: The study of reductive unfolding pathways of RNase A (Y92G mutant) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ymw | ||||||
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Title | The study of reductive unfolding pathways of RNase A (Y92G mutant) | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE | ||||||
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: 1.5 Å | ||||||
Authors | Xu, G. / Narayan, M. / Kurinov, I. / Ripoll, D.R. / Welker, E. / Khalili, M. / Ealick, S.E. / Scheraga, H.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 Title: A localized specific interaction alters the unfolding pathways of structural homologues. Authors: Xu, G. / Narayan, M. / Kurinov, I. / Ripoll, D.R. / Welker, E. / Khalili, M. / Ealick, S.E. / Scheraga, H.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ymw.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ymw.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 1ymw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ymw_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 1ymw_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 1ymw_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1ymw_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1ymw ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1ymw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13602.204 Da / Num. of mol.: 1 / Mutation: Y92G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Plasmid: PET22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: 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: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: Ammonium sulfate, Sodium chloride, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 23303 / Num. obs: 23303 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.36 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 838869.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 85.0412 Å2 / ksol: 0.495835 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
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Xplor file |
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