+Open data
-Basic information
Entry | Database: PDB / ID: 2bnk | ||||||
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Title | The structure of phage phi29 replication organizer protein p16.7 | ||||||
Components | EARLY PROTEIN GP16.7 | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information viral DNA genome replication / host cell membrane / DNA replication / host cell plasma membrane / DNA binding / membrane Similarity search - Function | ||||||
Biological species | BACILLUS PHAGE PHI29 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Albert, A. / Asensio, J.L. / Munoz-Espin, D. / Gonzalez, C. / Hermoso, J.A. / Villar, L. / Jimenez-Barbero, J. / Salas, M. / Meijer, W.J.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structure of the Functional Domain of {Varphi}29 Replication Organizer: Insights Into Oligomerization and DNA Binding. Authors: Asensio, J.L. / Albert, A. / Munoz-Espin, D. / Gonzalez, C. / Hermoso, J.A. / Villar, L. / Jimenez-Barbero, J. / Salas, M. / Meijer, W.J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bnk.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bnk.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bnk ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bnk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.0024, -0.0019), Vector: |
-Components
#1: Protein | Mass: 7937.970 Da / Num. of mol.: 2 / Fragment: RESIDUES 64-130 Source method: isolated from a genetically manipulated source Details: DSDNA AND SSDNA BINDING PROTEIN / Source: (gene. exp.) BACILLUS PHAGE PHI29 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P16517 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.75 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 5257 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.442 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.883 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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