+Open data
-Basic information
Entry | Database: PDB / ID: 1rhl | ||||||
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Title | RIBONUCLEASE T1 COMPLEXED WITH 2'GMP/G23A MUTANT | ||||||
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: 1.95 Å | ||||||
Authors | Huyghues-Despointes, B.M.P. / Langhorst, U. / Steyaert, J. / Pace, C.N. / Scholtz, J.M. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Hydrogen-exchange stabilities of RNase T1 and variants with buried and solvent-exposed Ala --> Gly mutations in the helix. Authors: Huyghues-Despointes, B.M. / Langhorst, U. / Steyaert, J. / Pace, C.N. / Scholtz, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rhl.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rhl.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rhl_validation.pdf.gz | 829 KB | Display | wwPDB validaton report |
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Full document | 1rhl_full_validation.pdf.gz | 829.3 KB | Display | |
Data in XML | 1rhl_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1rhl_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/1rhl ftp://data.pdbj.org/pub/pdb/validation_reports/rh/1rhl | HTTPS FTP |
-Related structure data
Related structure data | 1rgaS S: Starting model for refinement |
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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: 11108.722 Da / Num. of mol.: 1 / Mutation: G23A 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) / References: UniProt: P00651, EC: 3.1.27.3 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-2GP / |
#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: 2.24 Å3/Da / Density % sol: 44.98 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.2 / Details: 50 MM NAAC PH 4.2 2 MM CACL2 50 % MPD 2MM 2`GMP | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding | |||||||||||||||||||||||||||||||||||
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: May 15, 1998 |
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: 1.95→15 Å / Num. obs: 7378 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 6.84 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.95→2.04 Å / Redundancy: 6.75 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.3 / % possible all: 94.1 |
Reflection | *PLUS Num. measured all: 50578 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGA Resolution: 1.95→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.95→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.04 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: 15 Å / σ(F): 0 / % reflection Rfree: 10.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.232 / % reflection Rfree: 12.5 % / Rfactor Rwork: 0.222 / Rfactor obs: 0.222 |