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Yorodumi- PDB-3mxp: Crystal structure of Staphylococcal nuclease variant Delta+PHS T6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mxp | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS T62A at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Caro, J.A. / Schlessman, J.L. / Garcia-Moreno, E.B. / Heroux, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Cavities determine the pressure unfolding of proteins. Authors: Roche, J. / Caro, J.A. / Norberto, D.R. / Barthe, P. / Roumestand, C. / Schlessman, J.L. / Garcia, A.E. / Garcia-Moreno E, B. / Royer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mxp.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mxp.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 3mxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/3mxp ftp://data.pdbj.org/pub/pdb/validation_reports/mx/3mxp | HTTPS FTP |
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-Related structure data
Related structure data | 3mehC 3mhbC 3mvvC 3mz5C 3nk9C 3np8C 3nqtC 3nxwC 3osoC 3pmfC 3r3oC 3bdcS 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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Unit cell |
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-Components
#1: Protein | Mass: 16113.438 Da / Num. of mol.: 1 / Fragment: Deletion UNP residues 126-131 / Mutation: G50F,V51N,T62A,P117G,H124L,S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease |
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#2: Chemical | ChemComp-THP / |
#3: Chemical | ChemComp-CA / |
#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: 2.21 Å3/Da / Density % sol: 44.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→50 Å / Num. all: 18151 / Num. obs: 18151 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.092 / Χ2: 2.752 / Net I/σ(I): 13.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR | Rfactor: 36.11 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, T62A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20 A^2. Resolution: 1.61→32.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.826 / SU B: 2.004 / SU ML: 0.071 / SU R Cruickshank DPI: 0.103 / SU Rfree: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.56 Å2 / Biso mean: 25.935 Å2 / Biso min: 14.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→32.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.652 Å / Total num. of bins used: 20
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