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Yorodumi- PDB-6cbt: DnaG Primase C-terminal domain complex with SSB C-terminal peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cbt | ||||||
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Title | DnaG Primase C-terminal domain complex with SSB C-terminal peptide | ||||||
Components | DNA primase, single-stranded DNA-binding protein chimeraPrimase | ||||||
Keywords | REPLICATION / Primase / DnaG / Single-strand DNA-Binding Protein / SSB / Complex | ||||||
Function / homology | Function and homology information DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / replisome / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / single-stranded DNA binding ...DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / replisome / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Oakley, A.J. / Lo, A.T.Y. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To be Published Title: DnaG Primase C-terminal domain complex with SSB C-terminal peptide Authors: Oakley, A.J. / Lo, A.T.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cbt.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cbt.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/6cbt ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cbt | HTTPS FTP |
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-Related structure data
Related structure data | 6cbrC 6cbsC 1t3wS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18691.049 Da / Num. of mol.: 2 Fragment: DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 Gene: dnaG, dnaP, parB, b3066, JW3038, ssb_1, BUE81_14300, ERS085374_00666 Plasmid: pAL1402 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0ABS5, UniProt: A0A0K3FKM0 #2: Chemical | #3: Chemical | #4: 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: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953715 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953715 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→70 Å / Num. obs: 21786 / % possible obs: 96.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.702 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.057 / Rrim(I) all: 0.146 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3075 / Rpim(I) all: 0.23 / Rrim(I) all: 0.61 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1T3W Resolution: 2.1→45.742 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.742 Å
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Refine LS restraints |
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LS refinement shell |
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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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