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Yorodumi- PDB-3qoj: Cryogenic structure of Staphylococcal nuclease variant D+PHS/V23K -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qoj | ||||||
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Title | Cryogenic structure of Staphylococcal nuclease variant D+PHS/V23K | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdTp | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Robinson, A.C. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B. | ||||||
Citation | Journal: To be Published Title: Determinants of pKa values of internal ionizable groups: properties of ion pairs in the protein core Authors: Robinson, A.C. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B. / Castaneda, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qoj.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qoj.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qoj_validation.pdf.gz | 781.1 KB | Display | wwPDB validaton report |
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Full document | 3qoj_full_validation.pdf.gz | 781.9 KB | Display | |
Data in XML | 3qoj_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 3qoj_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qoj ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qoj | HTTPS FTP |
-Related structure data
Related structure data | 3bdcS S: Starting model for refinement |
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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: 16173.514 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23K,G50F,V51N,P117G,H124L,S128A, del(44-49) 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 |
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#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 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24% MPD, 25 mM potassium phosphate, pdTp (2 eq.), calcium chloride (3 eq.), pH 8, 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: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2009 Details: MERIDIONALLY-BENT FUSED SILICA MIRROR WITH PALLADIUM AND UNCOATED STRIPES VERTICALLY- FOCUSING AT 6.6:1 DEMAGNIFICATION |
Radiation | Monochromator: DOUBLE SILICON(111) CRYSTAL MONOCHROMATOR WITH CRYOGENICALLY- COOLED FIRST CRYSTAL AND SAGITTALLY-BENT SECOND CRYSTAL HORIZONTALLY-FOCUSING AT 3.3:1 DEMAGNIFICATION. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→23.65 Å / Num. all: 18219 / Num. obs: 18219 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 2069 / Rsym value: 0.252 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BDC Resolution: 1.6→23.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.301 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.094 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 mean: 23.602 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→23.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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