+Open data
-Basic information
Entry | Database: PDB / ID: 3gsp | ||||||
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Title | RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS + 3'-GMP, 4 DAYS | ||||||
Components | RIBONUCLEASE T1 | ||||||
Keywords | ENDORIBONUCLEASE / HYDROLASE | ||||||
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 | Zegers, I. / Wyns, L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography. Authors: Zegers, I. / Loris, R. / Dehollander, G. / Fattah Haikal, A. / Poortmans, F. / Steyaert, J. / Wyns, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gsp.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gsp.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/3gsp ftp://data.pdbj.org/pub/pdb/validation_reports/gs/3gsp | HTTPS FTP |
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-Related structure data
Related structure data | 1gspC 2gspC 4gspC 5gspC 6gspC 7gspC 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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-Components
#1: Protein | Mass: 11094.694 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH GUANOSINE 2',3' CYCLIC PHOSPHOROTHIOATE AND 3'GMP Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: P00651, EC: 3.1.27.3 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SGP / |
#4: Chemical | ChemComp-3GP / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | SGP IS THE SUBSTRATE AND 3GP THE PRODUCT OF A HYDROLYSIS REACTION TAKING PLACE IN THE CRYSTALS. ...SGP IS THE SUBSTRATE AND 3GP THE PRODUCT OF A HYDROLYSIS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 35.2 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.2 / Details: 20 MM NAAC PH 4.2 2 MM CACL2 55 % MPD | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / 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: 7964 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.052 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6 % / Mean I/σ(I) obs: 15 / Rsym value: 0.134 / % possible all: 92.1 |
Reflection | *PLUS Num. measured all: 63228 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 92.1 % / Rmerge(I) obs: 0.134 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGA Resolution: 1.9→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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