+Open data
-Basic information
Entry | Database: PDB / ID: 1rge | ||||||
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Title | HYDROLASE, GUANYLORIBONUCLEASE | ||||||
Components | RIBONUCLEASE | ||||||
Keywords | HYDROLASE (GUANYLORIBONUCLEASE) | ||||||
Function / homology | Function and homology information ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.15 Å | ||||||
Authors | Sevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Ribonuclease from Streptomyces aureofaciens at atomic resolution. Authors: Sevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Complex of Ribonuclease from Streptomyces Aureofaciens with 2'-Gmp at 1.7A Resolution Authors: Sevcik, J. / Hill, C.P. / Dauter, Z. / Wilson, K.S. #2: Journal: Eur.J.Biochem. / Year: 1993 Title: Complex of Ribonuclease Sa with a Cyclic Nucleotide and a Proposed Model for the Reaction Intermediate Authors: Sevcik, J. / Zegers, I. / Wyns, L. / Dauter, Z. / Wilson, K.S. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1991 Title: Determination and Restrained Least-Squares Refinement of the Structures of Ribonuclease Sa and its Complex with 3'-Guanylic Acid at 1.8 A Resolution Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G. #4: 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. #5: Journal: FEBS Lett. / Year: 1986 Title: Amino Acid Sequence Determination of Guanyl-Specific Ribonuclease Sa from Streptomyces Aureofaciens Authors: Shlyapnikov, S.V. / Both, V. / Kulikov, V.A. / Dementiev, A.A. / Sevcik, J. / Zelinka, J. #6: Journal: Biochim.Biophys.Acta / Year: 1971 Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. I. Isolation and Purification Authors: Bacova, M. / Zelinkova, E. / Zelinka, J. #7: Journal: Biochim.Biophys.Acta / Year: 1971 Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. II. Properties and Specificity Authors: Zelinkova, E. / Bacova, M. / Zelinka, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rge.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rge.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rge_validation.pdf.gz | 870.9 KB | Display | wwPDB validaton report |
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Full document | 1rge_full_validation.pdf.gz | 873.5 KB | Display | |
Data in XML | 1rge_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1rge_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/1rge ftp://data.pdbj.org/pub/pdb/validation_reports/rg/1rge | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.97076, 0.23453, 0.05116), Vector: |
-Components
#1: Protein | Mass: 10582.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces aureofaciens (bacteria) / References: UniProt: P05798, EC: 3.1.27.3 #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-2GP / | #4: Water | ChemComp-HOH / | Compound details | SECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS ...SECONDARY STRUCTURE BOUNDARIES | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.45 % | ||||||||||||||||||||
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Crystal grow | pH: 6.7 / Details: ROOM TEMPERATURE, PH 6.7, AMMONIUM SULFATE / Temp details: room temp | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.92 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Redundancy: 7.1 % / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Highest resolution: 1.15 Å / Num. obs: 62845 / % possible obs: 87.3 % / Num. measured all: 445145 / Biso Wilson estimate: 11.2 Å2 |
-Processing
Software |
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Refinement | Resolution: 1.15→10 Å / Num. parameters: 18013 / Num. restraintsaints: 21102 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOU RECORDS CONTAIN ANISOTROPIC DISPLACEMENT PARAMETERS U11 U22 U33 U23 U13 U12 (ANGSTROMS**2) MULTIPLIED BY 10000. ISOTROPIC EQUIVALENTS OF ANISOTROPIC TEMPERATURE FACTORS ARE ALSO PRESENTED IN THIS ENTRY.
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Solvent computation | Solvent model: BASED ON BABINET'S PRINCIPLE | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 13 / Occupancy sum non hydrogen: 1957 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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