[English] 日本語
Yorodumi- PDB-3r3o: Crystal structure of Staphylococcal nuclease variant Delta+PHS T6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r3o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS T62A at cryogenic temperature and with high redundancy | ||||||
Components | ThermonucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE / hyperstable variant / pdtp / pressure / cavity | ||||||
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 Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Caro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3r3o.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3r3o.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 3r3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/3r3o ftp://data.pdbj.org/pub/pdb/validation_reports/r3/3r3o | HTTPS FTP |
---|
-Related structure data
Related structure data | 3mehC 3mhbC 3mvvC 3mxpC 3mz5C 3nk9C 3np8C 3nqtC 3nxwC 3osoC 3pmfC 3bdcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16113.438 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) Mutation: UNP G132F,V133N,T144A,P199G,H206L,S210A,del(126-131) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00644, UniProt: Q8NXI6*PLUS, micrococcal nuclease |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-THP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.04 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 21% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 25, 2010 / Details: multilayer |
Radiation | Monochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 11069 / Num. obs: 11067 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.42 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.0333 / Net I/σ(I): 22.76 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.2658 / Mean I/σ(I) obs: 3.34 / Num. unique all: 347 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BDC Resolution: 1.9→31.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2127 / WRfactor Rwork: 0.1611 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8605 / SU B: 6.843 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1516 / SU Rfree: 0.1507 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 61.09 Å2 / Biso mean: 23.0704 Å2 / Biso min: 9.04 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|