+Open data
-Basic information
Entry | Database: PDB / ID: 2pnh | ||||||
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Title | Escherichia coli PriB E39A variant | ||||||
Components | Primosomal replication protein n | ||||||
Keywords | DNA BINDING PROTEIN / beta barrel / OB fold | ||||||
Function / homology | Function and homology information pre-primosome complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / response to radiation / single-stranded DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Lopper, M.E. / Keck, J.L. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: A hand-off mechanism for primosome assembly in replication restart. Authors: Lopper, M. / Boonsombat, R. / Sandler, S.J. / Keck, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pnh.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pnh.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 2pnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/2pnh ftp://data.pdbj.org/pub/pdb/validation_reports/pn/2pnh | HTTPS FTP |
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-Related structure data
Related structure data | 1txyS 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: 11683.435 Da / Num. of mol.: 2 / Mutation: E39A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: priB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07013 #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: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8% polyethylene glycol 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 10045 / Num. obs: 9302 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Χ2: 2.011 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.7 / Num. unique all: 725 / Rsym value: 0.438 / Χ2: 1.461 / % possible all: 75.1 |
-Phasing
Phasing MR | Rfactor: 0.321 / Cor.coef. Fo:Fc: 0.784 / Cor.coef. Io to Ic: 0.762
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TXY Resolution: 2.25→19.95 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.902 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.427 / ESU R Free: 0.268 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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 mean: 65.987 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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