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Yorodumi- PDB-1gov: RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gov | ||||||
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Title | RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS | ||||||
Components | RIBONUCLEASE | ||||||
Keywords | HYDROLASE / ENDORIBONUCLEASE / NUCLEASE | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | BACILLUS INTERMEDIUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Polyakov, K.M. / Lebedev, A.A. / Pavlovsky, A.G. / Sanishvili, R.G. / Dodson, G.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: The Structure of Substrate-Free Microbial Ribonuclease Binase and of its Complexes with 3'Gmp and Sulfate Ions Authors: Polyakov, K.M. / Lebedev, A.A. / Okorokov, A.L. / Panov, K.I. / Schulga, A.A. / Pavlovsky, A.G. / Karpeisky, M.Y.A. / Dodson, G.G. #1: Journal: Trends Biochem.Sci. / Year: 1990 Title: Comparison of Active Sites of Some Microbial Ribonucleases: Structural Basis for Guanylic Specificity Authors: Sevcik, J. / Sanishvili, R.G. / Pavlovsky, A.G. / Polyakov, K.M. #2: Journal: FEBS Lett. / Year: 1983 Title: Three-Dimensional Structure of Ribonuclese from Balillus Intermedius 7P at 3A Resolution Authors: Pavlovsky, A.G. / Vagin, A.A. / Vainshtein, B.K. / Chepurnova, N.K. / Karpeisky, M.Y. #3: Journal: Trends Biochem.Sci. / Year: 1983 Title: The Structural and Sequence Homology of Family of Microbial Ribonucleases Authors: Hill, C. / Dodson, G. / Heinemann, U. / Saenger, W. / Mitsui, Y. / Nakamura, K. / Borisov, S. / Tischenko, G. / Polyakov, K. / Pavlovsky, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gov.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gov.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gov_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 1gov_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 1gov_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1gov_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/1gov ftp://data.pdbj.org/pub/pdb/validation_reports/go/1gov | HTTPS FTP |
-Related 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 | Mass: 12974.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS Source: (natural) BACILLUS INTERMEDIUS (bacteria) / References: UniProt: P00649, EC: 3.1.27.3 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.75 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→10 Å / Num. obs: 18100 / % possible obs: 100 % / Redundancy: 2 % |
Reflection | *PLUS Lowest resolution: 55.7 Å / Num. obs: 18301 / % possible obs: 99.8 % / Num. measured all: 18301 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 97.9 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 3.427 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NONE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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