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Open data
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Basic information
Entry | Database: PDB / ID: 6gsp | ||||||
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Title | RIBONUCLEASE T1/3'-GMP, 15 WEEKS | ||||||
![]() | RIBONUCLEASE T1 | ||||||
![]() | ENDORIBONUCLEASE / HYDROLASE / RIBONUCLEASE / ENDONUCLEASE | ||||||
Function / homology | ![]() hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zegers, I. / Wyns, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32 KB | Display | ![]() |
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PDB format | ![]() | 23.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gspC ![]() 2gspC ![]() 3gspC ![]() 4gspC ![]() 5gspC ![]() 7gspC ![]() 1rgaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: COMPLEXED WITH GUANOSINE-3'-PHOSPHATE / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-3GP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||
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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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 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: 2.2→20 Å / Num. obs: 5517 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.082 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.7 / Rsym value: 0.224 / % possible all: 94.7 |
Reflection | *PLUS Num. measured all: 11191 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 94.7 % / Rmerge(I) obs: 0.224 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RGA Resolution: 2.2→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: 19.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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