[English] 日本語
Yorodumi- PDB-3zqo: Crystal structure of the small terminase oligomerization core dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zqo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 3) | ||||||
Components | TERMINASE SMALL SUBUNIT | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / MOLECULAR MOTOR / DNA PACKAGING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS PHAGE SF6 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Buttner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Alonso, J.C. / Antson, A.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural Basis for DNA Recognition and Loading Into a Viral Packaging Motor. Authors: Buttner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Ebong, I.O. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Robinson, C.V. / Alonso, J.C. / Antson, A.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zqo.cif.gz | 416.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zqo.ent.gz | 344.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqo ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqo | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zqmSC 3zqnC 3zqpC 3zqqC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8067.110 Da / Num. of mol.: 18 / Fragment: OLIGOMERIZATION CORE DOMAIN, RESIDUES 53-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS PHAGE SF6 (virus) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q1EJR8, UniProt: P68928*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % / Description: NONE |
---|---|
Crystal grow | Details: 2.7 M (NH4)2SO4, 0.2 M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 3, 2008 / Details: BENT COLLIMATING MIRROR AND TOROID | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 1.68→22.1 Å / Num. obs: 127549 / % possible obs: 85.6 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8 | |||||||||||||||
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 98 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZQM Resolution: 1.68→22.1 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.191 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.71 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→22.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|