+Open data
-Basic information
Entry | Database: PDB / ID: 2bir | ||||||
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Title | ADDITIVITY OF SUBSTRATE BINDING IN RIBONUCLEASE T1 (Y42A MUTANT) | ||||||
Components | RIBONUCLEASE T1 | ||||||
Keywords | RIBONUCLEASE / HYDROLASE / NUCLEASE / 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: 2.3 Å | ||||||
Authors | Doumen, J. / Steyaert, J. / Loverix, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: Additivity of protein-guanine interactions in ribonuclease T1. Authors: Loverix, S. / Doumen, J. / Steyaert, J. #1: Journal: J.Biol.Chem. / Year: 1988 Title: Three-Dimensional Structure of the Ribonuclease T1 2'-Gmp Complex at 1.9-A Resolution Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W. #2: Journal: Nature / Year: 1982 Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex: An X-Ray Study Authors: Heinemann, U. / Saenger, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bir.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bir.ent.gz | 23.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/2bir ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2bir | HTTPS FTP |
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-Related structure data
Related structure data | 1birS 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: 10958.588 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / References: UniProt: P00651 |
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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: 2.23 Å3/Da / Density % sol: 44.79 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.2 / Details: pH 4.20 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 6, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→10 Å / Num. obs: 4313 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.107 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.239 / % possible all: 50 |
Reflection | *PLUS % possible obs: 93 % / Rmerge(I) obs: 0.107 |
Reflection shell | *PLUS % possible obs: 49.7 % / Rmerge(I) obs: 0.239 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BIR Resolution: 2.3→10 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESOLUTION-DEPENDENT WEIGHTING USED. BULK SOLVENT MODEL USED.
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Displacement parameters | Biso mean: 21.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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