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Yorodumi- PDB-1low: X-ray structure of the H40A mutant of Ribonuclease T1 complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1low | ||||||
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Title | X-ray structure of the H40A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate | ||||||
Components | Guanyl-specific ribonuclease T1 | ||||||
Keywords | HYDROLASE / RNase / catalytic dyad / nucleophile activation / ab initio calculations | ||||||
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 | Mignon, P. / Steyaert, J. / Loris, R. / Geerlings, P. / Loverix, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study Authors: Mignon, P. / Steyaert, J. / Loris, R. / Geerlings, P. / Loverix, S. | ||||||
History |
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Remark 999 | The isozyme of RNase T1 used here contains a lysine at position 25. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1low.cif.gz | 33.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1low.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 1low.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1low_validation.pdf.gz | 761.3 KB | Display | wwPDB validaton report |
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Full document | 1low_full_validation.pdf.gz | 761.5 KB | Display | |
Data in XML | 1low_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1low_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1low ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1low | HTTPS FTP |
-Related structure data
Related structure data | 1lovC 1loyC 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: 11027.625 Da / Num. of mol.: 1 / Mutation: H40A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Plasmid: pMC / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / References: UniProt: P00651, EC: 3.1.27.3 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-3GP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: MPD,CaCl2,sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||
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 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 2001 |
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→15 Å / Num. all: 7614 / Num. obs: 7614 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.94 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 3.7 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 7613 / % possible obs: 99.31 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGA Resolution: 1.9→22.8 Å / Cross valid method: THROUGHOUT / σ(F): 0.001 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→22.8 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.205 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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