+Open data
-Basic information
Entry | Database: PDB / ID: 1bvi | ||||||
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Title | RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP | ||||||
Components | PROTEIN (RIBONUCLEASE T1) | ||||||
Keywords | HYDROLASE / ENDORIBONUCLEASE / RIBONUCLEASE / ENDONUCLEASE | ||||||
Function / homology | Function and homology information hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Langhorst, U. / Loris, R. / Denisov, V.P. / Doumen, J. / Roose, P. / Maes, D. / Halle, B. / Steyaert, J. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Dissection of the structural and functional role of a conserved hydration site in RNase T1. Authors: Langhorst, U. / Loris, R. / Denisov, V.P. / Doumen, J. / Roose, P. / Maes, D. / Halle, B. / Steyaert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bvi.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bvi.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bvi_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1bvi_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1bvi_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1bvi_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/1bvi ftp://data.pdbj.org/pub/pdb/validation_reports/bv/1bvi | HTTPS FTP |
-Related structure data
Related structure data | 2hohC 3hohC 4hohC 5hohC 1rgaS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 11094.694 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH GUANOSINE-2'-MONOPHOSPHATE / Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / References: UniProt: P00651, EC: 3.1.27.3 #2: Chemical | ChemComp-2GP / #3: Chemical | #4: 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: 2.04 Å3/Da / Density % sol: 39.81 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.2 / Details: 25 MM NAAC PH 4.2 6.25 MM CACL2 47.5 % MPD | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: DUAL SLITS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 28421 / % possible obs: 96.7 % / Redundancy: 4.88 % / Rsym value: 0.061 / Net I/σ(I): 15.86 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 3.26 % / Mean I/σ(I) obs: 4.75 / Rsym value: 0.313 / % possible all: 77.1 |
Reflection | *PLUS Num. measured all: 138761 / Rmerge(I) obs: 0.061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGA Resolution: 1.9→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 10.5 % / Rfactor Rwork: 0.348 |