+Open data
-Basic information
Entry | Database: PDB / ID: 1hyf | ||||||
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Title | RIBONUCLEASE T1 V16A MUTANT IN COMPLEX WITH SR2+ | ||||||
Components | GUANYL-SPECIFIC RIBONUCLEASE T1 | ||||||
Keywords | HYDROLASE / Ribonuclease / stability / metal binding | ||||||
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: 1.7 Å | ||||||
Authors | De Swarte, J. / De Vos, S. / Langhorst, U. / Steyaert, J. / Loris, R. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: The contribution of metal ions to the conformational stability of ribonuclease T1: crystal versus solution. Authors: Deswarte, J. / De Vos, S. / Langhorst, U. / Steyaert, J. / Loris, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hyf.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hyf.ent.gz | 22.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/1hyf ftp://data.pdbj.org/pub/pdb/validation_reports/hy/1hyf | 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: 11066.642 Da / Num. of mol.: 1 / Mutation: V16A Source method: isolated from a genetically manipulated source 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-SR / |
#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: 2.16 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: MPD, calcium chloride, acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: graphite monochromator |
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: 1.7→25 Å / Num. all: 10427 / Num. obs: 10427 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.77 % / Biso Wilson estimate: 20.56 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.07 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 5 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.18 / Num. unique all: 921 / % possible all: 85 |
Reflection | *PLUS Num. measured all: 81045 |
Reflection shell | *PLUS % possible obs: 85 % / Num. unique obs: 921 / Num. measured obs: 4600 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25 Å / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.1881 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |