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Yorodumi- PDB-3bir: DISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 BY ASN AND GL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bir | ||||||
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Title | DISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 BY ASN AND GLN SUBSTITUTIONS | ||||||
Components | RIBONUCLEASE T1 | ||||||
Keywords | ENDONUCLEASE / HYDROLASE / RIBONUCLEASE T1 / MUTATION | ||||||
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: 1.8 Å | ||||||
Authors | Doumen, J. / Steyaert, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Dissecting histidine interactions of ribonuclease T1 with asparagine and glutamine replacements: analysis of double mutant cycles at one position. Authors: De Vos, S. / Doumen, J. / Langhorst, U. / Steyaert, J. #1: Journal: J.Mol.Biol. / Year: 1992 Title: His92Ala Mutation in Ribonuclease T1 Induces Segmental Flexibility. An X-Ray Study Authors: Koellner, G. / Choe, H.W. / Heinemann, U. / Grunert, H.P. / Zouni, A. / Hahn, U. / Saenger, W. #2: 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. #3: 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 | 3bir.cif.gz | 33.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bir.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bir_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 3bir_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 3bir_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 3bir_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3bir ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3bir | HTTPS FTP |
-Related structure data
Related structure data | 5birC 1birS 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: 11070.650 Da / Num. of mol.: 1 / Mutation: H92N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: SYNTHETIC GENE / Plasmid: PMC5-RT1 / Gene (production host): SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P00651, EC: 3.1.27.3 | ||||
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#2: Chemical | #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: 2.13 Å3/Da / Density % sol: 42.2 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.2 Details: VAPOR DIFFUSION, NAOAC PH 4.2, 20 MG/ML PROTEIN, 45 % MPD 2.5 MM CACL2, 20 MM GPS | ||||||||||||||||||||||||||||||||||||
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: Nov 6, 1995 / Details: DUAL SLITS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→10 Å / Num. obs: 4313 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 14.2 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 Highest resolution: 1.8 Å / Num. obs: 8680 / % possible obs: 98.8 % / Num. measured all: 28974 / Rmerge(I) obs: 0.107 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 95.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BIR Resolution: 1.8→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
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Displacement parameters | Biso mean: 15.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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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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