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Yorodumi- PDB-3zqq: Crystal structure of the full-length small terminase from a SPP1-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zqq | ||||||
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Title | Crystal structure of the full-length small terminase from a SPP1-like bacteriophage | ||||||
Components | TERMINASE SMALL SUBUNIT | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / DNA PACKAGING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS PHAGE SF6 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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 |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zqq.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zqq.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zqq_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 3zqq_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 3zqq_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3zqq_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqq ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqq | HTTPS FTP |
-Related structure data
Related structure data | 3zqmC 3zqnC 3zqoC 3zqpSC 2cmpS C: citing same article (ref.) 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: 18069.576 Da / Num. of mol.: 3 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): BL21(DE3) / References: UniProt: Q1EJR8, UniProt: P68928*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 60 % Description: MR WAS PERFORMED USING THREE NEIGHBORING SUBUNITS |
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Crystal grow | Details: 0.2 M MGCL2, 8 % PEG 2000, 8 % PEG 550MME, 0.1 M TRIS PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 4.01→107 Å / Num. obs: 3308 / % possible obs: 62 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 4.01→4.23 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.1 / % possible all: 18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2CMP AND 3ZQP Resolution: 4→107 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE THIRD DNA-BINDING DOMAIN (DBD OF CHAIN B) IS NOT SUFFICIENTLY DEFINED IN THE ELECTRON DENSITY AND WAS NOT MODELED.
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Solvent computation | Bsol: 207.145 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 220 Å2
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Refinement step | Cycle: LAST / Resolution: 4→107 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.01→4.23 Å / Rfactor Rfree: 0.2011 / Rfactor Rwork: 0.2026 / Total num. of bins used: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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