+Open data
-Basic information
Entry | Database: PDB / ID: 1eqn | ||||||
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Title | E.COLI PRIMASE CATALYTIC CORE | ||||||
Components | DNA PRIMASEPrimase | ||||||
Keywords | TRANSFERASE / Toprim domain / Rossmann fold | ||||||
Function / homology | Function and homology information DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / replisome / DNA replication, synthesis of primer / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA binding ...DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / replisome / DNA replication, synthesis of primer / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | ||||||
Authors | Podobnik, M. / McInerney, P. / O'Donnell, M. / Kuriyan, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases. Authors: Podobnik, M. / McInerney, P. / O'Donnell, M. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eqn.cif.gz | 301.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eqn.ent.gz | 257.2 KB | Display | PDB format |
PDBx/mmJSON format | 1eqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eqn ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eqn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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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5 |
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Unit cell |
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Details | The biological assembly is a monomer constructed from either chain A, B, C, D or E. |
-Components
#1: Protein | Mass: 36620.941 Da / Num. of mol.: 5 / Fragment: CATALYTIC CORE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PPROEX-HTA / Production host: Escherichia coli (E. coli) References: UniProt: P0ABS5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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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: 2.42 Å3/Da / Density % sol: 49.21 % Description: For the refinement the data from lambda 1 (0.98636) were taken. | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 50 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃Details: drop consists of equal volume of protein and reservoir solutions PH range low: 8.5 / PH range high: 7.9 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98636, 0.97939, 0.97900, 0.96526 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 1999 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→20 Å / Num. all: 273234 / Num. obs: 272858 / % possible obs: 97.6 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 73.637 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.3 | |||||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.207 / Num. unique all: 13126 / % possible all: 90.8 | |||||||||||||||
Reflection | *PLUS Num. obs: 40874 / Num. measured all: 273234 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 90.8 % |
-Processing
Software |
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Refinement | Resolution: 2.9→500 Å / σ(F): 2 Stereochemistry target values: Engh & Huber, Hendrickson W.A. and Konnert J.H. Details: used standard crystallographic residual
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Refinement step | Cycle: LAST / Resolution: 2.9→500 Å
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Refine LS restraints |
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