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Open data
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Basic information
Entry | Database: PDB / ID: 1i70 | ||||||
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Title | CRYSTAL STRUCTURE OF RNASE SA Y86F MUTANT | ||||||
![]() | GUANYL-SPECIFIC RIBONUCLEASE SA | ||||||
![]() | HYDROLASE / MUTANT | ||||||
Function / homology | ![]() ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sevcik, J. / Urbanikova, L. | ||||||
![]() | ![]() 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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Remark 999 | SEQUENCE ACCORDING TO THE AUTHOR, THE ORIGINAL SEQUENCE OF THE RNASE SA IN THE SEQUENCE DATABASE ...SEQUENCE ACCORDING TO THE AUTHOR, THE ORIGINAL SEQUENCE OF THE RNASE SA IN THE SEQUENCE DATABASE SWISSPROT ENTRY P05798 IS WRONG. RESIDUE 72 IS THR, NOT CYS. THIS ISSUE IS DISCUSSED IN THE PAPER: SEVCIK J., DAUTER Z., LAMZIN V.S. AND WILSON K.S. (1996), ACTA CRYSTALLOGR. D52, 327-344 ON THE BASIS OF ATOMIC RESOLUTION REFINEMENT. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.8 KB | Display | ![]() |
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PDB format | ![]() | 41.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.4 KB | Display | ![]() |
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Full document | ![]() | 431.1 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i8vC ![]() 1rggS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: Y86F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||
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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 293K | ||||||||||||||||||||
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: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1999 |
Radiation | Monochromator: FOCUSING CURVED MONO. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30.7 Å / Num. all: 21828 / Num. obs: 84702 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 7.1 / % possible all: 95.5 |
Reflection | *PLUS Num. obs: 21859 / Num. measured all: 84702 |
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Processing
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Refinement | Method to determine structure: STARTING MODEL WAS USED WITHOUT MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGG Resolution: 1.7→30.7 Å / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.09 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 16.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 30.7 Å / Luzzati sigma a obs: 0.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / % reflection obs: 95.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_planar_d / Dev ideal: 0.04 / Dev ideal target: 0.05 |