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Yorodumi- PDB-1ymn: The study of reductive unfolding pathways of RNase A (Y92L mutant) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ymn | ||||||
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Title | The study of reductive unfolding pathways of RNase A (Y92L 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: 1.45 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 | 1ymn.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ymn.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ymn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ymn_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 1ymn_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 1ymn_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1ymn_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1ymn ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1ymn | 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: 13658.310 Da / Num. of mol.: 1 / Mutation: Y92L 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 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.08 % |
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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: May 26, 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: 1.45→30 Å / Num. all: 29537 / Num. obs: 28902 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.224 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1780197.73 / 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: 73.6989 Å2 / ksol: 0.467223 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.5 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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