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- PDB-1goy: HYDROLASE(ENDORIBONUCLEASE)RIBONUCLEASE BI(G SPECIFIC ENDONUCLEAS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1goy | ||||||
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Title | HYDROLASE(ENDORIBONUCLEASE)RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) (E.C.3.1.27.-) COMPLEXED WITH GUANOSINE-3'-PHOSPHATE (3'-GMP) | ||||||
![]() | RIBONUCLEASE | ||||||
![]() | HYDROLASE / ENDORIBONUCLEASE / NUCLEASE | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Polyakov, K.M. / Lebedev, A.A. / Pavlovsky, A.G. / Sanishvili, R.G. / Dodson, G.G. | ||||||
![]() | ![]() 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: ![]() Title: The Crystall Structure of Bacterial Ribonuclease Binase Authors: Pavlovsky, A.G. / Sanishvili, R.G. / Borisova, S.N. / Strokopytov, B.V. / Vagin, A.A. / Chepurnova, N.K. / Vainshtein, B.K. #3: 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. #4: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.3 KB | Display | ![]() |
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PDB format | ![]() | 45.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 811.3 KB | Display | ![]() |
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Full document | ![]() | 812.6 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: MICROORGANISM / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-3GP / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
Detector | Type: SYTNEX P21 |
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: 14982 / % possible obs: 99 % / Redundancy: 2 % |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 24.9 Å / Num. obs: 15152 / % possible obs: 82.9 % / Num. measured all: 15152 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 34.2 % / Mean I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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