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- PDB-4c8o: Binary complex of the large fragment of DNA polymerase I from The... -

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Basic information

Entry
Database: PDB / ID: 4c8o
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 2)
Components
  • 5'-D(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'
  • 5'-D(*TP*TP*CP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3'
  • DNA POLYMERASE I, THERMOSTABLE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA POLYMERASE / UNNATURAL BASE PAIR / ARTIFICIAL BASE PAIR / BINARY COMPLEX / KLENTAQ
Function / homology
Function and homology information


nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / double-strand break repair / 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 / DNA polymerase 1 / 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 / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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 / OTHER / Resolution: 1.75 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 / reflns / reflns_shell
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 2.1May 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'
C: 5'-D(*TP*TP*CP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,47113
Polymers68,6173
Non-polymers85410
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-108.1 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.802, 99.185, 203.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2006-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA POLYMERASE I, THERMOSTABLE / TAQ POLYMERASE 1


Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, RESIDUES 293-832
Source method: isolated from a genetically manipulated source
Details: OPEN CONFORMATION OF ENZYME TRAPPED BY CRYSTAL CONTACTS
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*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3' / PRIMER


Mass: 3384.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*TP*TP*CP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3' / TEMPLATE


Mass: 4295.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 246 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details5'-TT 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: 2.39 Å3/Da / Density % sol: 48.53 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 30% W/V PEG 5000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 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: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.75→48.2 Å / Num. obs: 66214 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 35.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.73
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.99 / CC1/2: 0.527 / % possible all: 99.2

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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: 1.75→47.876 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 3300 5 %
Rwork0.1846 --
obs0.1861 66155 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.57 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 472 45 236 5044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054979
X-RAY DIFFRACTIONf_angle_d0.9646857
X-RAY DIFFRACTIONf_dihedral_angle_d16.0521949
X-RAY DIFFRACTIONf_chiral_restr0.037748
X-RAY DIFFRACTIONf_plane_restr0.004840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7750.42861250.44182575X-RAY DIFFRACTION100
1.775-1.80150.41661470.40292572X-RAY DIFFRACTION98
1.8015-1.82970.37591310.37242551X-RAY DIFFRACTION100
1.8297-1.85970.3891290.35622624X-RAY DIFFRACTION99
1.8597-1.89170.37881370.32672556X-RAY DIFFRACTION100
1.8917-1.92610.31331460.31732576X-RAY DIFFRACTION99
1.9261-1.96320.32271300.312596X-RAY DIFFRACTION99
1.9632-2.00330.30091270.2772593X-RAY DIFFRACTION100
2.0033-2.04680.29661330.26022615X-RAY DIFFRACTION99
2.0468-2.09440.28721300.24092598X-RAY DIFFRACTION100
2.0944-2.14680.31161310.2222595X-RAY DIFFRACTION100
2.1468-2.20490.25961430.21022615X-RAY DIFFRACTION99
2.2049-2.26970.24821460.20452606X-RAY DIFFRACTION100
2.2697-2.3430.22381370.19882579X-RAY DIFFRACTION100
2.343-2.42670.23711180.19692661X-RAY DIFFRACTION100
2.4267-2.52390.21051250.19512617X-RAY DIFFRACTION100
2.5239-2.63870.27211270.20242638X-RAY DIFFRACTION100
2.6387-2.77790.25041890.2072590X-RAY DIFFRACTION100
2.7779-2.95190.22741360.21052662X-RAY DIFFRACTION100
2.9519-3.17970.2321410.20052619X-RAY DIFFRACTION100
3.1797-3.49970.20971490.17672655X-RAY DIFFRACTION100
3.4997-4.00580.17611260.14792686X-RAY DIFFRACTION100
4.0058-5.04610.14111400.12642684X-RAY DIFFRACTION99
5.0461-47.89390.16381570.14052792X-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)
12.5358-0.7131-0.3511.166-0.83932.9345-0.12660.00010.04910.19440.21510.1995-0.2034-0.933-0.07580.30280.05990.01350.58480.04420.3253-24.7832-30.81526.782
21.77420.90560.37791.4140.96261.54730.04270.10890.2466-0.04040.0663-0.1103-0.24310.185-0.12640.37960.00850.02740.35310.04880.37157.2761-22.69138.5906
31.31380.1624-0.0510.6797-0.58021.8441-0.07160.24660.0542-0.0131-0.0104-0.1280.04260.26040.10380.26920.025-0.00650.42930.00530.29056.9291-32.56515.6503
44.49691.9725-2.32932.01490.46245.3112-0.30121.0108-0.0265-0.49960.2496-0.155-0.163-0.630.09790.62870.03460.00630.42290.03070.3962-0.1986-13.787636.5147
56.0508-1.902-2.03847.06384.56835.38650.50781.32890.3636-0.9405-0.5467-0.0947-0.7116-0.7023-0.11070.65770.14160.01650.57690.06470.44580.0797-14.402535.2181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 293 THROUGH 433 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 434 THROUGH 588 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 589 THROUGH 832 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 102 THROUGH 111 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 204 THROUGH 215 )

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