+Open data
-Basic information
Entry | Database: PDB / ID: 1i8v | ||||||
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Title | CRYSTAL STRUCTURE OF RNASE SA Y80F MUTANT | ||||||
Components | GUANYL-SPECIFIC RIBONUCLEASE SA | ||||||
Keywords | HYDROLASE / mutant | ||||||
Function / homology | Function and homology information ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / STARTING MODEL WAS USED WITHOUT MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Sevcik, J. / Urbanikova, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Tyrosine hydrogen bonds make a large contribution to protein stability. Authors: Pace, C.N. / Horn, G. / Hebert, E.J. / Bechert, J. / Shaw, K. / Urbanikova, L. / Scholtz, J.M. / Sevcik, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i8v.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i8v.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 1i8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i8v ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i8v | HTTPS FTP |
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-Related structure data
Related structure data | 1i70C 1rggS 1i8w 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10566.492 Da / Num. of mol.: 2 / Mutation: Y80F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P05798, EC: 3.1.27.3 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: AMMONIUM SULFATE, MONOSODIUM PHOSPHATE, DISODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding / PH range low: 7.2 / PH range high: 7 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.044 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1999 |
Radiation | Monochromator: SI 111 CHANNEL-CUT XTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.044 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→19.65 Å / Num. all: 52680 / Num. obs: 52680 / % possible obs: 94.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.391 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.09 |
Reflection shell | Resolution: 1.25→1.26 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.28 / % possible all: 83.5 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: STARTING MODEL WAS USED WITHOUT MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGG Resolution: 1.25→19.6 Å / SU B: 0.717 / SU ML: 0.03 / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.25→19.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |