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- PDB-4cch: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 4cch
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with d5SICS as templating nucleotide
Components
  • 5'-D(*AP*AP*CP*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP* C)-3'
  • 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3'
  • DNA POLYMERASE I, THERMOSTABLE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / UNNATURAL NUCLEOTIDE / ARTIFICIAL NUCLEOTIDE / BINARY COMPLEX / KLENTAQ
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / 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
FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 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 23, 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / refine / reflns / reflns_shell / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: DNA POLYMERASE I, THERMOSTABLE
B: 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3'
C: 5'-D(*AP*AP*CP*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP* C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8199
Polymers69,5193
Non-polymers3006
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-10.5 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.262, 114.262, 91.537
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA POLYMERASE I, THERMOSTABLE / 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 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3'


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PRIMER' / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*AP*CP*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP* C)-3'


Mass: 4964.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 128 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE THREE 5'-NUCLEOTIDES (AAC) OF THE TEMPLATE ARE 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: 2.91 Å3/Da / Density % sol: 57.76 % / Description: NONE
Crystal growpH: 8
Details: 20% W/V PEG 8000, 0.1M TRIS PH 8.0, 0.2M MAGNESIUM FORMATE, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2013 / 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→49.5 Å / Num. obs: 22906 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 47.01 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.16
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 0.65 / CC1/2: 0.523 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3m8s

3m8s


Resolution: 2.55→43.526 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 27.89 / Stereochemistry target values: ML
Details: THE N-TERMINAL AMINO ACID 293 AND THE LOOP BETWEEN RESIDUES 647-659 ARE NOT MODELLED DUE TO DISORDER
RfactorNum. reflection% reflection
Rfree0.2608 2303 5.3 %
Rwork0.207 --
obs0.2098 22879 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.39 Å2
Refinement stepCycle: LAST / Resolution: 2.55→43.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 511 19 122 4857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054883
X-RAY DIFFRACTIONf_angle_d0.776708
X-RAY DIFFRACTIONf_dihedral_angle_d16.3811900
X-RAY DIFFRACTIONf_chiral_restr0.032735
X-RAY DIFFRACTIONf_plane_restr0.003801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.60550.35511470.34832569X-RAY DIFFRACTION99
2.6055-2.66610.37821470.34392592X-RAY DIFFRACTION100
2.6661-2.73280.38021350.33752524X-RAY DIFFRACTION100
2.7328-2.80660.33491600.2942580X-RAY DIFFRACTION100
2.8066-2.88920.34681200.29642591X-RAY DIFFRACTION100
2.8892-2.98240.33961390.27992606X-RAY DIFFRACTION100
2.9824-3.0890.29161720.26152561X-RAY DIFFRACTION100
3.089-3.21260.24491080.23732610X-RAY DIFFRACTION100
3.2126-3.35880.27571530.22882576X-RAY DIFFRACTION100
3.3588-3.53580.27691310.21812578X-RAY DIFFRACTION100
3.5358-3.75720.24141520.19872597X-RAY DIFFRACTION100
3.7572-4.04710.26171620.18072548X-RAY DIFFRACTION100
4.0471-4.4540.20221640.15942564X-RAY DIFFRACTION100
4.454-5.09770.24551160.15452595X-RAY DIFFRACTION100
5.0977-6.41930.2251450.16692599X-RAY DIFFRACTION100
6.4193-43.5320.21331520.15052566X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.44970.3190.57652.2181-0.89851.75020.03570.1497-0.7914-0.2653-0.1808-0.28050.9350.33530.09870.83820.05050.13910.28520.05710.603742.4654-45.2876-17.8884
21.64950.156-0.00880.1866-0.45331.25610.0052-0.26690.6854-0.0530.0134-0.1743-0.40910.2443-0.00140.6039-0.16420.1270.32110.00350.646237.4497-15.36360.6713
34.03252.67520.01552.0476-0.52764.20540.2387-0.65211.15390.3585-0.17720.3134-0.3894-1.2699-0.2290.61130.07960.16030.53040.04040.755513.2117-18.4397-8.2613
41.52650.2899-0.50460.7801-0.62352.7520.01370.24570.0272-0.1265-0.0595-0.15420.0949-0.53880.02250.4641-0.10580.09550.39690.0930.36921.0678-29.067-15.4419
59.94941.1891-1.24626.09721.71881.1317-0.64430.945-0.19410.4971-0.1346-1.4075-0.02480.25260.73260.43930.0125-0.07480.47570.16650.709947.1068-30.95697.2199
67.0119-1.14735.5070.4247-0.39925.4068-0.015-0.50780.4363-0.01010.01240.2635-0.1995-0.3827-0.04650.4187-0.04420.12820.19960.01680.424532.4023-19.65683.5045
72.4482-2.11470.74413.09271.39993.52040.35840.00070.72250.1820.0646-0.0361-0.3198-0.2163-0.37950.4324-0.08290.17590.35530.06290.312531.7962-26.5491-1.6988
82.0613-3.6806-1.8176.60583.22841.6039-0.5042-0.51920.42841.15170.6202-0.60540.07750.639-0.16440.444-0.1064-0.15380.51130.0010.560247.5741-26.022712.6498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 295 THROUGH 433 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 434 THROUGH 588 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 589 THROUGH 700 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 701 THROUGH 832 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 101 THROUGH 106 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 107 THROUGH 111 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 205 THROUGH 210 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 211 THROUGH 216 )

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