+Open data
-Basic information
Entry | Database: PDB / ID: 1bir | ||||||
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Title | RIBONUCLEASE T1, PHE 100 TO ALA MUTANT COMPLEXED WITH 2' GMP | ||||||
Components | RIBONUCLEASE T1 | ||||||
Keywords | ENDORIBONUCLEASE / HYDROLASE / NUCLEASE | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Doumen, J. / Gonciarz, M. / Zegers, I. / Loris, R. / Wyns, L. / Steyaert, J. | ||||||
Citation | Journal: Protein Sci. / Year: 1996 Title: A catalytic function for the structurally conserved residue Phe 100 of ribonuclease T1. Authors: Doumen, J. / Gonciarz, M. / Zegers, I. / Loris, R. / Wyns, L. / Steyaert, J. #1: Journal: Biochemistry / Year: 1992 Title: Role of Histidine-40 in Ribonuclease T1 Catalysis: Three-Dimensional Structures of the Partially Active His40Lys Mutant Authors: Zegers, I. / Verhelst, P. / Choe, H.W. / Steyaert, J. / Heinemann, U. / Saenger, W. / Wyns, L. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bir.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bir.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bir ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bir | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9963, 0.0852, -0.0065), Vector: |
-Components
#1: Protein | Mass: 11018.598 Da / Num. of mol.: 2 / Mutation: F100A Source method: isolated from a genetically manipulated source Details: COMPLEX WITH 2'-GMP / Source: (gene. exp.) Aspergillus oryzae (mold) Description: STEYAERT ET AL. (1990) BIOCHEMISTRY 29, 9064-9072 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.04 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.2 / Method: vapor diffusion, sitting drop / Details: used to seeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.056 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 17890 / % possible obs: 99.7 % / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS Highest resolution: 1.82 Å / Lowest resolution: 1.9 Å / % possible obs: 100 % / Rmerge(I) obs: 0.056 |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 14.84 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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