+Open data
-Basic information
Entry | Database: PDB / ID: 1bu4 | ||||||
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Title | RIBONUCLEASE 1 COMPLEX WITH 2'GMP | ||||||
Components | RIBONUCLEASE T1 | ||||||
Keywords | ENDORIBONUCLEASE / HYDROLASE | ||||||
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 | Loris, R. / Devos, S. / Langhorst, U. / Decanniere, K. / Bouckaert, J. / Maes, D. / Transue, T.R. / Steyaert, J. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: Conserved water molecules in a large family of microbial ribonucleases. Authors: Loris, R. / Langhorst, U. / De Vos, S. / Decanniere, K. / Bouckaert, J. / Maes, D. / Transue, T.R. / Steyaert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bu4.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bu4.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1bu4 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1bu4 | HTTPS FTP |
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-Related 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: 11094.694 Da / Num. of mol.: 1 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 | 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: 2.26 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.2 / Method: vapor diffusion, hanging drop / Details: Zegers, I., (1998) Nat. Struct. Biol., 5, 280. | ||||||||||||||||||||||||||||||||||||
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 RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 7907 / % possible obs: 95.6 % / Redundancy: 5.5 % / Rsym value: 0.139 / Net I/σ(I): 12.66 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.47 / Rsym value: 0.583 / % possible all: 92.2 |
Reflection | *PLUS Num. obs: 7853 / Redundancy: 5.6 % / Num. measured all: 44006 / Rmerge(I) obs: 0.139 |
Reflection shell | *PLUS Rmerge(I) obs: 0.583 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rfree: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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