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Yorodumi- PDB-3zqm: Crystal structure of the small terminase oligomerization core dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zqm | ||||||
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Title | Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 1) | ||||||
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 / SAD / Resolution: 1.85 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zqm.cif.gz | 233 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zqm.ent.gz | 201.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zqm_validation.pdf.gz | 473.8 KB | Display | wwPDB validaton report |
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Full document | 3zqm_full_validation.pdf.gz | 474.7 KB | Display | |
Data in XML | 3zqm_validation.xml.gz | 24 KB | Display | |
Data in CIF | 3zqm_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqm ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqm | HTTPS FTP |
-Related 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: 8067.110 Da / Num. of mol.: 10 / 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: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Details: 0.1 M MALONATE/IMIDAZOLE/BORIC ACID BUFFER SYSTEM PH 7.0, 25 % PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.971557 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.971557 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 52842 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.3 / % possible all: 86 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.85→80.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.286 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.483 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→80.06 Å
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Refine LS restraints |
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