+Open data
-Basic information
Entry | Database: PDB / ID: 1jvv | ||||||
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Title | CRYSTAL STRUCTURE OF RIBONUCLEASE A (RETRO-SOAKED FORM) | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE / PROTEIN DYNAMICS / PROTEIN STRUCTURE-FUNCTION | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Vitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L. | ||||||
Citation | Journal: Proteins / Year: 2002 Title: Reversible Substrate-Induced Domain Motions in Ribonuclease A Authors: Vitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L. #1: Journal: Protein Sci. / Year: 2000 Title: Productive and Non-Productive Binding to Ribonuclease A: X-Ray Structure of Two Complexes with Uridylyl(2',5')Guanosine Authors: Vitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L. #2: Journal: Protein Sci. / Year: 1998 Title: Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine Authors: Vitagliano, L. / Adinolfi, S. / Riccio, A. / Sica, F. / Zagari, A. / Mazzarella, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jvv.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jvv.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1jvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jvv ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jvv | HTTPS FTP |
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-Related structure data
Related structure data | 1jvtC 1jvuSC 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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2 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, sodium citrate, pH 5.00, VAPOR DIFFUSION, HANGING DROP at 298K. THE CRYSTAL WAS PREVIOUSLY SOAKED WITH 2'-CMP AND THEN RETRO-SOAKED BY WASHING OUT THE NUCLEOTIDE | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 | ||||||||||||||||||||||||||||||||||||
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: ENRAF-NONIUS FR591 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Sep 22, 1999 |
Radiation | Monochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 29907 / Num. obs: 11257 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 87 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 89 % / Num. measured all: 29907 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JVU Resolution: 2.2→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å
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Refinement | *PLUS Lowest resolution: 8 Å / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.26 |