+Open data
-Basic information
Entry | Database: PDB / ID: 4haa | ||||||
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Title | Structure of Ribonuclease Binase Glu43Ala/Phe81Ala Mutant | ||||||
Components | Ribonuclease | ||||||
Keywords | HYDROLASE / endoribonuclease | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus intermedius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Polyakov, K.M. / Trofimov, A.A. / Mitchevich, V.A. / Dorovatovskii, P.V. / Schulga, A.A. / Makarov, A.A. / Tkach, E.N. / Goncharuk, D.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure and functional studies of the ribonuclease binase Glu43Ala/Phe81Ala mutant. Authors: Mitkevich, V.A. / Schulga, A.A. / Trofimov, A.A. / Dorovatovskii, P.V. / Goncharuk, D.A. / Tkach, E.N. / Makarov, A.A. / Polyakov, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4haa.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4haa.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 4haa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/4haa ftp://data.pdbj.org/pub/pdb/validation_reports/ha/4haa | HTTPS FTP |
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-Related structure data
Related structure data | 1govS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12093.490 Da / Num. of mol.: 4 / Fragment: UNP residues 54-162 / Mutation: E43A/F81A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus intermedius (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P00649, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: 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: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 10 mg/mL protein, reservoir: 0.1 M citric acid, pH 3.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.983 Å | |||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 10, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.89→60 Å / Num. all: 37967 / Num. obs: 37967 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 | |||||||||||||||
Reflection shell | Resolution: 1.89→2.01 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.49 / Num. unique all: 5895 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GOV Resolution: 1.9→18.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.02 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.062 Å2
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Refine analyze | Luzzati coordinate error free: 0.027 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→18.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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