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- PDB-4c8l: Binary complex of the large fragment of DNA polymerase I from The... -

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Basic information

Entry
Database: PDB / ID: 4c8l
TitleBinary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the artificial base pair dNaM-d5SICS at the postinsertion site (sequence context 1)
Components
  • 5'-D(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'
  • 5'-D(*AP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3'
  • DNA POLYMERASE I, THERMOSTABLE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA POLYMERASE / UNNATURAL BASE PAIR / ARTIFICIAL BASE PAIR / 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
DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2.0Aug 23, 2017Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_detector / reflns / reflns_shell
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _diffrn_detector.type / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 2.1Dec 20, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn_type.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(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'
C: 5'-D(*AP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,25414
Polymers68,3613
Non-polymers89311
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-79 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.614, 100.543, 204.341
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 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(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'


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


Mass: 4055.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 290 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.04 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 28% W/V PEG 5000MME

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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: Jun 21, 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: 1.7→48.8 Å / Num. obs: 74923 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 32.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.57
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.85 / CC1/2: 0.492 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SZ2

3sz2


Resolution: 1.7→48.394 Å / SU ML: 0.37 / σ(F): 21.66 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 7192 5 %
Rwork0.1886 --
obs0.1898 74501 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 493 52 279 5115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115015
X-RAY DIFFRACTIONf_angle_d1.2396895
X-RAY DIFFRACTIONf_dihedral_angle_d16.0681963
X-RAY DIFFRACTIONf_chiral_restr0.052749
X-RAY DIFFRACTIONf_plane_restr0.007843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.63262320.61594633X-RAY DIFFRACTION100
1.7193-1.73960.57332430.55764446X-RAY DIFFRACTION100
1.7396-1.76080.52642260.56314640X-RAY DIFFRACTION100
1.7608-1.78310.51662660.52584449X-RAY DIFFRACTION100
1.7831-1.80650.55072600.49384472X-RAY DIFFRACTION100
1.8065-1.83130.40162310.42954587X-RAY DIFFRACTION100
1.8313-1.85750.38072260.38444525X-RAY DIFFRACTION100
1.8575-1.88520.3782300.33684584X-RAY DIFFRACTION100
1.8852-1.91460.33222560.31014472X-RAY DIFFRACTION100
1.9146-1.9460.34762580.28854585X-RAY DIFFRACTION100
1.946-1.97960.31482280.26134542X-RAY DIFFRACTION100
1.9796-2.01560.27192260.24714564X-RAY DIFFRACTION100
2.0156-2.05440.27342160.24434557X-RAY DIFFRACTION100
2.0544-2.09630.29682520.24074507X-RAY DIFFRACTION100
2.0963-2.14190.3022140.22544588X-RAY DIFFRACTION100
2.1419-2.19170.23272350.21174521X-RAY DIFFRACTION100
2.1917-2.24650.21342650.20164517X-RAY DIFFRACTION100
2.2465-2.30720.24422440.19074602X-RAY DIFFRACTION100
2.3072-2.37510.20992310.18624476X-RAY DIFFRACTION100
2.3751-2.45180.22422080.18634632X-RAY DIFFRACTION100
2.4518-2.53940.23732230.17354516X-RAY DIFFRACTION100
2.5394-2.64110.20822040.17844594X-RAY DIFFRACTION100
2.6411-2.76130.20812920.17874482X-RAY DIFFRACTION100
2.7613-2.90680.22072900.18454483X-RAY DIFFRACTION100
2.9068-3.08890.2082440.17194554X-RAY DIFFRACTION100
3.0889-3.32740.20932370.16934587X-RAY DIFFRACTION100
3.3274-3.66210.16782240.15564534X-RAY DIFFRACTION100
3.6621-4.19180.17062340.14664517X-RAY DIFFRACTION100
4.1918-5.28020.15642440.12764549X-RAY DIFFRACTION100
5.2802-48.41320.14292530.14114519X-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)
11.6738-0.29830.09910.7576-0.48811.8227-0.0125-0.018-0.0230.02720.20920.2444-0.0428-0.8321-0.16280.2595-0.0185-0.00610.52460.10830.3372-23.21-32.076527.3395
20.81630.4021-0.06351.8743-0.11541.7243-0.00460.00560.24630.04390.1131-0.0949-0.38740.426-0.07710.364-0.120.01870.3358-0.00120.322211.9056-18.576842.4081
31.24550.1217-0.25940.8555-0.86922.92680.04230.27970.0625-0.0377-0.0758-0.08830.09380.35480.02420.2304-0.0041-0.00650.31570.0220.26356.0072-32.628617.019
40.519-0.429-0.62780.67860.67431.43270.09880.24180.22140.2624-0.1540.0143-0.3799-0.3648-0.07580.5518-0.00450.02870.31860.02670.43790.057-15.383434.9173
52.25390.90430.2760.87840.00532.68060.0920.2650.44830.11990.0793-0.0681-0.293-0.1719-0.29960.45650.02490.03090.2520.02710.45950.4362-15.820934.5662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 293 THROUGH 452 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 453 THROUGH 562 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 563 THROUGH 832 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 102 THROUGH 112 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 203 THROUGH 215 )

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