[English] 日本語
Yorodumi- PDB-9cik: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cik | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V23R/L36D at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / STAPHYLOCOCCAL NUCLEASE / ARGININE / ION PAIR | ||||||
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 / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Zhang, Y. / Schlessman, J.L. / SIegler, M.A. / Garcia-Moreno E., B. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS V23R/L36D at cryogenic temperature Authors: Zhang, Y. / Schlessman, J.L. / Robinson, A.C. / Garcia-Moreno E., B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9cik.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9cik.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 9cik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cik_validation.pdf.gz | 786.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9cik_full_validation.pdf.gz | 787.4 KB | Display | |
Data in XML | 9cik_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 9cik_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/9cik ftp://data.pdbj.org/pub/pdb/validation_reports/ci/9cik | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16203.459 Da / Num. of mol.: 1 / Mutation: V23R, L36D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc, SACOL0860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HHM4, micrococcal nuclease |
---|---|
#2: Chemical | ChemComp-THP / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.88 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 28% MPD, 25 mM Potassium Phosphate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5418 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 15, 2022 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20.11 Å / Num. obs: 10282 / % possible obs: 99.9 % / Redundancy: 16 % / Rmerge(I) obs: 0.016 / Rsym value: 0.049 / Net I/σ(I): 53.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.85 / Num. unique obs: 1030 / Rsym value: 0.305 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.975 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.257 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→19.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|