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- PDB-3e0d: Insights into the Replisome from the Crystral Structure of the Te... -

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Entry
Database: PDB / ID: 3e0d
TitleInsights into the Replisome from the Crystral Structure of the Ternary Complex of the Eubacterial DNA Polymerase III alpha-subunit
Components
  • DNA polymerase III subunit alphaDNA polymerase III holoenzyme
  • DNA substrate primer strand
  • DNA substrate template strand
KeywordsTRANSFERASE/DNA / OB fold / nucleotidyl transferase / polymerase / beta barrel / Cytoplasm / DNA replication / DNA-directed DNA polymerase / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cytoplasm
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain ...Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 Å
AuthorsWing, R.A. / Bailey, S. / Steitz, T.A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Insights into the Replisome from the Structure of a Ternary Complex of the DNA Polymerase III alpha-Subunit.
Authors: Wing, R.A. / Bailey, S. / Steitz, T.A.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA substrate template strand
D: DNA substrate primer strand
E: DNA substrate template strand
F: DNA substrate primer strand
A: DNA polymerase III subunit alpha
B: DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,68810
Polymers304,6266
Non-polymers1,0634
Water0
1
C: DNA substrate template strand
D: DNA substrate primer strand
A: DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,8445
Polymers152,3133
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA substrate template strand
F: DNA substrate primer strand
B: DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,8445
Polymers152,3133
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.546, 149.546, 163.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: DNA chain DNA substrate template strand


Mass: 8287.300 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA substrate primer strand


Mass: 6411.167 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein DNA polymerase III subunit alpha / DNA polymerase III holoenzyme / E.C.2.7.7.7


Mass: 137614.391 Da / Num. of mol.: 2 / Mutation: D20N, D212N, I539F, Q540E, V541A, V542E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: dnaE / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XDH5, DNA-directed DNA polymerase
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 16 - 21% PEG 400, 100 mM CaCl2, 100 mM HEPES, VAPOR DIFFUSION, SITTING DROP, temperature 289.15K
PH range: 6.9 - 7.2
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2CaCl211
3HEPES11
4H2O11
5PEG 40012
6CaCl212
7HEPES12
8H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11
SYNCHROTRONAPS 24-ID-C21
Detector
IDDetectorDate
1CCDMar 9, 2007
2CCDMar 9, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionHighest resolution: 4.6 Å / Num. obs: 20097
Reflection shellHighest resolution: 4.6 Å

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.6→50 Å
Details: Some peptide bond distances are outside the normal range. The data in the structure factor file are twinned. Twinning operator= k, h, -l twinning fraction= 0.45
RfactorNum. reflection
Rfree0.271 -
Rwork0.287 -
obs-20097
Refinement stepCycle: LAST / Resolution: 4.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18336 1584 62 0 19982

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