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- PDB-4c8m: Binary complex of the large fragment of DNA polymerase I from The... -

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Basic information

Entry
Database: PDB / ID: 4c8m
TitleBinary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair d5SICS-dNaM at the postinsertion site (sequence context 2)
Components
  • LARGE FRAGMENT OF TAQ DNA POLYMERASE I
  • PRIMER, 5'-D(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*BMNP)-3'
  • TEMPLATE, 5'-D(*TP*TP*CP* LHOP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3'
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / UNNATURAL BASE PAIR
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
DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.568 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 / pdbx_struct_conn_angle / 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 / _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: LARGE FRAGMENT OF TAQ DNA POLYMERASE I
B: PRIMER, 5'-D(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*BMNP)-3'
C: TEMPLATE, 5'-D(*TP*TP*CP* LHOP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,41413
Polymers68,6173
Non-polymers79710
Water6,305350
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-60.9 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.374, 101.456, 204.543
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-2009-

HOH

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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 natural source / Source: (natural) THERMUS AQUATICUS (bacteria) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3367.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain TEMPLATE, 5'-D(*TP*TP*CP* LHOP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3'


Mass: 4312.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 360 molecules

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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.48 Å3/Da / Density % sol: 50.35 % / 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
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: 1.57→49.2 Å / Num. obs: 94841 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.48
Reflection shellResolution: 1.57→1.66 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.78 / CC1/2: 0.531 / % possible all: 97.1

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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: 1.568→49.236 Å / SU ML: 0.28 / σ(F): 21.06 / Phase error: 30.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 9061 5 %
Rwork0.1785 --
obs0.18 94768 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.22 Å2
Refinement stepCycle: LAST / Resolution: 1.568→49.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 492 47 350 5180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115038
X-RAY DIFFRACTIONf_angle_d1.2836941
X-RAY DIFFRACTIONf_dihedral_angle_d16.9071980
X-RAY DIFFRACTIONf_chiral_restr0.055755
X-RAY DIFFRACTIONf_plane_restr0.008848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5684-1.58630.48922700.48424670X-RAY DIFFRACTION79
1.5863-1.60490.45162550.46865360X-RAY DIFFRACTION93
1.6049-1.62450.40043030.44985595X-RAY DIFFRACTION96
1.6245-1.64510.43372480.42715740X-RAY DIFFRACTION98
1.6451-1.66670.37663050.38565764X-RAY DIFFRACTION99
1.6667-1.68950.37862890.36125791X-RAY DIFFRACTION99
1.6895-1.71370.33032970.34345819X-RAY DIFFRACTION100
1.7137-1.73930.35922960.3425807X-RAY DIFFRACTION100
1.7393-1.76640.35193090.32545873X-RAY DIFFRACTION100
1.7664-1.79540.35543320.32275700X-RAY DIFFRACTION100
1.7954-1.82640.31923420.29445891X-RAY DIFFRACTION100
1.8264-1.85960.30832700.2625809X-RAY DIFFRACTION100
1.8596-1.89530.29312840.24015849X-RAY DIFFRACTION100
1.8953-1.9340.27373530.22815790X-RAY DIFFRACTION100
1.934-1.97610.27343110.2065804X-RAY DIFFRACTION100
1.9761-2.0220.22542780.19595873X-RAY DIFFRACTION100
2.022-2.07260.24693080.19565857X-RAY DIFFRACTION100
2.0726-2.12870.25612650.18485800X-RAY DIFFRACTION100
2.1287-2.19130.22793110.17875796X-RAY DIFFRACTION100
2.1913-2.2620.23973410.1725841X-RAY DIFFRACTION100
2.262-2.34290.19943240.15985825X-RAY DIFFRACTION100
2.3429-2.43670.18762660.15535833X-RAY DIFFRACTION100
2.4367-2.54760.17322810.16055859X-RAY DIFFRACTION100
2.5476-2.68190.21012760.16945845X-RAY DIFFRACTION100
2.6819-2.84990.20184010.17375748X-RAY DIFFRACTION100
2.8499-3.06990.2043210.18295804X-RAY DIFFRACTION100
3.0699-3.37880.23883130.18325850X-RAY DIFFRACTION100
3.3788-3.86750.18242920.16125806X-RAY DIFFRACTION100
3.8675-4.8720.15513070.13175837X-RAY DIFFRACTION100
4.872-49.26070.15333130.1385825X-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)
12.2951-0.45070.18580.7872-0.31221.4979-0.1107-0.3648-0.08420.14590.15880.1996-0.0678-0.7287-0.0510.26730.01450.01090.47810.0420.2705-23.0276-31.97127.3351
21.40930.60910.40921.74110.55561.79540.02610.02530.11040.08630.1087-0.2074-0.14110.3021-0.14530.3010.02080.02250.3553-0.00630.28779.1713-22.40539.6505
31.03540.3036-0.09420.4666-0.35271.3579-0.02460.10960.0271-0.0049-0.0274-0.07880.0520.16660.06670.25030.0123-0.00380.26710.00480.26746.9771-32.329514.3332
44.7971-0.3838-1.7420.8917-1.13323.956-0.06911.0904-0.1697-0.122-0.0580.07760.0545-0.51650.10940.4323-0.05-0.05150.3488-0.05790.34690.3414-14.580535.2644
55.4017-3.986-3.8494.94874.98694.94110.2851.04650.1101-0.5446-0.1078-0.0753-0.3987-0.6967-0.14720.5555-0.01280.02560.44920.02390.44380.353-14.107835.1676
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 603 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 604 THROUGH 832 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 102 THROUGH 112 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 204 THROUGH 215 )

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