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- PDB-3mhb: Crystal structure of Staphylococcal nuclease variant Delta+PHS L3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mhb | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS L38A at cryogenic temperature | ||||||
![]() | Thermonuclease | ||||||
![]() | HYDROLASE / hyperstable variant / pdtp / cavity / pressure | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caro, J.A. / Schlessman, J.L. / Garcia-Moreno, E.B. / Heroux, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.3 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.8 KB | Display | ![]() |
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Full document | ![]() | 809.4 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mehC ![]() 3mvvC ![]() 3mxpC ![]() 3mz5C ![]() 3nk9C ![]() 3np8C ![]() 3nqtC ![]() 3nxwC ![]() 3osoC ![]() 3pmfC ![]() 3r3oC ![]() 3bdcS ![]() 3m87 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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Unit cell |
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Components
#1: Protein | Mass: 16101.383 Da / Num. of mol.: 1 / Fragment: Deletion UNP residues 126-131 / Mutation: L38A,G50F,V51N,P117G,H124L,S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-THP / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.71 % |
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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 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→60 Å / Num. all: 20512 / Num. obs: 20512 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.052 / Χ2: 2.138 / Net I/σ(I): 17.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR | Rfactor: 37.03 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, L36A, L37A, L38A, K64A, D77A T82A, Y91A, Y113A, V114A, Y115A and N118A; all b-factors were reset to 20. Resolution: 1.55→30.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.842 / SU B: 1.557 / SU ML: 0.058 / SU R Cruickshank DPI: 0.09 / SU Rfree: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.098 / 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: 53.02 Å2 / Biso mean: 22.598 Å2 / Biso min: 12.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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