+Open data
-Basic information
Entry | Database: PDB / ID: 1dde | ||||||
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Title | STRUCTURE OF THE DNAG CATALYTIC CORE | ||||||
Components | DNA PRIMASE | ||||||
Keywords | TRANSFERASE / TOPRIM / 3-HELIX BUNDLE / DNA-BINDING PROTEIN / RNA POLYMERASE / REPLICATION PROTEIN / PRIMASE | ||||||
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 / 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 / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Keck, J.L. / Roche, D.D. / Lynch, A.S. / Berger, J.M. | ||||||
Citation | Journal: Science / Year: 2000 Title: Structure of the RNA polymerase domain of E. coli primase. Authors: Keck, J.L. / Roche, D.D. / Lynch, A.S. / Berger, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dde.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dde.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dde_validation.pdf.gz | 368.3 KB | Display | wwPDB validaton report |
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Full document | 1dde_full_validation.pdf.gz | 374 KB | Display | |
Data in XML | 1dde_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1dde_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1dde ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1dde | HTTPS FTP |
-Related 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: 38222.254 Da / Num. of mol.: 1 / Fragment: 36 KDA CATALYTIC CORE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PREP4 DERIVATIVE / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 References: UniProt: P0ABS5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||||
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#2: Chemical | ChemComp-Y1 / #3: Water | ChemComp-HOH / | Nonpolymer details | Y(2+) IONS ARE PRESENT IN THE PUTATIVE ACTIVE SITE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.53 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM YCL2, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 40211 / Num. obs: 39886 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.287 / % possible all: 94.6 |
Reflection | *PLUS Num. measured all: 236503 |
Reflection shell | *PLUS % possible obs: 94.6 % / Mean I/σ(I) obs: 3.7 |
-Processing
Software |
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Refinement | Resolution: 1.7→20 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / σ(F): 0 / Rfactor obs: 0.209 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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