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Yorodumi- PDB-7lwr: Structural and Biochemical Insight into Assembly of Molecular Mot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lwr | ||||||
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Title | Structural and Biochemical Insight into Assembly of Molecular Motors Involved in Viral DNA Packaging | ||||||
Components | Terminase, small subunit | ||||||
Keywords | VIRAL PROTEIN / DNA Packaging / Terminase | ||||||
Function / homology | Bacteriophage lambda, Nu1, terminase small subunit / Phage DNA packaging protein Nu1 / Putative DNA-binding domain superfamily / host cell cytoplasm / Winged helix-like DNA-binding domain superfamily / DNA binding / ATP binding / Terminase, small subunit Function and homology information | ||||||
Biological species | Enterobacteria phage P21 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ortega, M.E. | ||||||
Citation | Journal: To Be Published Title: Structural and Biochemical Insight into Assembly of Molecular Motors Involved in Viral DNA Packaging Authors: Ortega, M.E. / Randriamihaja, A. / Rossen, N. / Brannon, J.P. / Marquez, C. / West, R. / Dabbagh, S. / Robles, R. / LeGue, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lwr.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lwr.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 7lwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lwr_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 7lwr_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 7lwr_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 7lwr_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/7lwr ftp://data.pdbj.org/pub/pdb/validation_reports/lw/7lwr | HTTPS FTP |
-Related structure data
Related structure data | 7lw0SC 7lxsC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 6223.146 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P21 (virus) / Gene: 1, nohA / Production host: Escherichia coli (E. coli) / References: UniProt: P68654 |
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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: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 2.5 M ammonium sulfate, 5% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jul 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→21.7 Å / Num. obs: 21002 / % possible obs: 99.8 % / Redundancy: 2.68 % / CC1/2: 0.987 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 2.35→3.5 Å / Num. unique obs: 19898 / CC1/2: 0.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LW0 Resolution: 2.35→21.69 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.425 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 233.77 Å2 / Biso mean: 19.641 Å2 / Biso min: 6.28 Å2
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Refinement step | Cycle: final / Resolution: 2.35→21.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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