[English] 日本語
Yorodumi- PDB-6zpb: Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and two ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zpb | ||||||
---|---|---|---|---|---|---|---|
Title | Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and two catalytic Co2+ ions | ||||||
Components | DatZ | ||||||
Keywords | VIRAL PROTEIN / S-2L / HD phosphohydrolase / DatZ | ||||||
Function / homology | Chem-3D1 / : Function and homology information | ||||||
Biological species | Cyanophage S-2L (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72097384171 Å | ||||||
Authors | Czernecki, D. / Legrand, P. / Delarue, M. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA. Authors: Czernecki, D. / Legrand, P. / Tekpinar, M. / Rosario, S. / Kaminski, P.A. / Delarue, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zpb.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zpb.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 6zpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zpb_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6zpb_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6zpb_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 6zpb_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zpb ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zpb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6|||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20612.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanophage S-2L (virus) / Production host: Escherichia coli (E. coli) | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-3D1 / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.29 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 1.5 M LiSO4; 100 mM HEPES; 10 mM CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.033202 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018 / Details: KB Mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033202 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→40.44 Å / Num. obs: 21613 / % possible obs: 98.4 % / Redundancy: 14.2 % / Biso Wilson estimate: 14.0930917762 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.022 / Rrim(I) all: 0.086 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.72→1.77 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 1400 / CC1/2: 0.939 / Rpim(I) all: 0.137 / Rrim(I) all: 0.338 / % possible all: 88 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.72097384171→40.4358636633 Å / SU ML: 0.165812802632 / Cross valid method: FREE R-VALUE / σ(F): 1.45045910224 / Phase error: 16.9899637983 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5063621561 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72097384171→40.4358636633 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|