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- PDB-4c8n: Binary complex of the large fragment of DNA polymerase I from The... -

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Basic information

Entry
Database: PDB / ID: 4c8n
TitleBinary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3)
Components
  • LARGE FRAGMENT OF TAQ DNA POLYMERASE I
  • PRIMER, 5'-D(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'
  • TEMPLATE, 5'-D(*TP*TP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3'
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / UNNATURAL BASE PAIR / ARTIFICIAL BASE PAIR / BINARY COMPLEX
Function / homology
Function and homology information


nucleoside binding / double-strand break repair via alternative nonhomologous end joining / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.88 Å
AuthorsBetz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Romesberg, F.E. / Marx, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structural Insights Into DNA Replication without Hydrogen Bonds.
Authors: Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Romesberg, F.E. / Marx, A.
History
DepositionOct 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Atomic model / Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LARGE FRAGMENT OF TAQ DNA POLYMERASE I
B: PRIMER, 5'-D(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'
C: TEMPLATE, 5'-D(*TP*TP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2879
Polymers68,6563
Non-polymers6306
Water3,657203
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-72 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.617, 101.096, 204.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LARGE FRAGMENT OF TAQ DNA POLYMERASE I / TAQ POLYMERASE 1 / LARGE FRAGMENT OF TAQ DNA POLYMERASE I


Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, RESIDUES 293-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Plasmid: PGDR11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain PRIMER, 5'-D(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'


Mass: 3368.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain TEMPLATE, 5'-D(*TP*TP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3'


Mass: 4350.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 209 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details5'-T OF THE TEMPLATE IS NOT RESOLVED IN THE STRUCTURE

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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: 2.47 Å3/Da / Density % sol: 50.31 % / Description: NONE
Crystal growpH: 7.5
Details: 1.2M LITHIUM SULFATE, 2% W/V PEG 1000, 50MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2012 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 1.88→49.1 Å / Num. obs: 55373 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 37.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.1
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.476 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.88→49.069 Å / SU ML: 0.34 / σ(F): 88.62 / Phase error: 33.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 2772 5 %
Rwork0.1956 --
obs0.1975 55305 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 1.88→49.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 495 35 203 5024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074976
X-RAY DIFFRACTIONf_angle_d1.0626839
X-RAY DIFFRACTIONf_dihedral_angle_d17.2361947
X-RAY DIFFRACTIONf_chiral_restr0.039747
X-RAY DIFFRACTIONf_plane_restr0.005836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.91240.43931370.41362370X-RAY DIFFRACTION93
1.9124-1.94720.43871480.3952578X-RAY DIFFRACTION98
1.9472-1.98470.43611240.36542581X-RAY DIFFRACTION100
1.9847-2.02520.39721320.35892629X-RAY DIFFRACTION100
2.0252-2.06920.38971390.3362632X-RAY DIFFRACTION100
2.0692-2.11730.34831230.3032603X-RAY DIFFRACTION100
2.1173-2.17030.3551350.2742618X-RAY DIFFRACTION100
2.1703-2.2290.30661370.24962605X-RAY DIFFRACTION100
2.229-2.29460.32551510.24092593X-RAY DIFFRACTION100
2.2946-2.36860.28411360.22942626X-RAY DIFFRACTION100
2.3686-2.45330.27381160.21412653X-RAY DIFFRACTION100
2.4533-2.55150.23231260.20822641X-RAY DIFFRACTION100
2.5515-2.66760.25371290.21222636X-RAY DIFFRACTION100
2.6676-2.80820.2621850.21112609X-RAY DIFFRACTION100
2.8082-2.98420.29441360.21932662X-RAY DIFFRACTION100
2.9842-3.21450.24781460.2082621X-RAY DIFFRACTION100
3.2145-3.53790.18861470.18042670X-RAY DIFFRACTION100
3.5379-4.04970.18811280.15922700X-RAY DIFFRACTION100
4.0497-5.10130.17731400.13732698X-RAY DIFFRACTION100
5.1013-49.08530.16651570.14822808X-RAY DIFFRACTION100

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