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Yorodumi- PDB-1cjq: X-RAY CRYSTALLOGRAPHIC STUDIES OF THE DENATURATION OF THE DENATUR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cjq | ||||||
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Title | X-RAY CRYSTALLOGRAPHIC STUDIES OF THE DENATURATION OF THE DENATURATION OF RIBONUCLEASE S. | ||||||
Components | (PROTEIN (RIBONUCLEASE S)) x 2 | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / DENATURATION | ||||||
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 | synthetic construct (others) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ratnaparkhi, G.S. / Varadarajan, R. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: X-ray crystallographic studies of the denaturation of ribonuclease S. Authors: Ratnaparkhi, G.S. / Varadarajan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cjq.cif.gz | 35.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cjq.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 1cjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/1cjq ftp://data.pdbj.org/pub/pdb/validation_reports/cj/1cjq | HTTPS FTP |
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-Related structure data
Related structure data | 1cjrC 1rnvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1752.944 Da / Num. of mol.: 1 / Fragment: S PEPTIDE / Source method: isolated from a natural source / Details: SYNTHETIC S PEPTIDE / Source: (natural) synthetic construct (others) / References: UniProt: P61823 |
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#2: Protein | Mass: 11294.749 Da / Num. of mol.: 1 / Fragment: S PROTEIN / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.81 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.75 Details: THE RNASE S CRYSTAL HAS BEEN STABILIZED BY GLUTARALDEHYDE CROSSLINKING AND THEN THE CRYSTAL HAS BEEN SOAKED IN 5M UREA., pH 4.75 DATA COLLECTED ON A CRYSTAL SOAKED IN 5M UREA. THE CRYSTAL ...Details: THE RNASE S CRYSTAL HAS BEEN STABILIZED BY GLUTARALDEHYDE CROSSLINKING AND THEN THE CRYSTAL HAS BEEN SOAKED IN 5M UREA., pH 4.75 DATA COLLECTED ON A CRYSTAL SOAKED IN 5M UREA. THE CRYSTAL WAS STABILIZED BY GLUTARALDEHYDE CROSSLINKING | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: unknown / Details: Kim, E.E., (1992) Biochemistry, 31, 12304. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→15 Å / Num. obs: 2233 / % possible obs: 76.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 53.1 Å2 / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 3→3.2 Å / % possible all: 49.3 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RNV Resolution: 3→15 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 27.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 1 / % reflection Rfree: 14.7 % / Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.237 / % reflection Rfree: 18.7 % / Rfactor Rwork: 0.217 |