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- PDB-7omb: Crystal structure of KOD DNA Polymerase in a ternary complex with... -

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Basic information

Entry
Database: PDB / ID: 7omb
TitleCrystal structure of KOD DNA Polymerase in a ternary complex with a p/t duplex containing an extended 5' single stranded template overhang
Components
  • DNA polymerase
  • Primer
  • Template
KeywordsREPLICATION / ternary complex / DNA polymerase
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / exonuclease activity / DNA-templated DNA replication / endonuclease activity / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / B family DNA polymerase, thumb domain / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 ...DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / B family DNA polymerase, thumb domain / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / Topoisomerase I; Chain A, domain 4 / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 Å
AuthorsBetz, K. / Kropp, H.M. / Diederichs, K. / Marx, A.
CitationJournal: Chembiochem / Year: 2021
Title: Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase.
Authors: Kropp, H.M. / Ludmann, S. / Diederichs, K. / Betz, K. / Marx, A.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Category: citation / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Feb 16, 2022Group: Structure summary / Category: entity / Item: _entity.pdbx_description / _entity.pdbx_ec
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: Template
P: Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,20215
Polymers100,1323
Non-polymers1,07012
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-41 kcal/mol
Surface area36010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.081, 147.153, 71.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-971-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase


Mass: 90060.461 Da / Num. of mol.: 1 / Mutation: Asp141Ala Glu143Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: pol, TK0001 / Production host: Escherichia coli (E. coli) / References: UniProt: P77933, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain Template


Mass: 6470.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Primer


Mass: 3601.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 289 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus E7: 0.12 M ethylene glycols (0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol), 0.1 M sodium HEPES/MOPS pH 7.5, 50 % (v/v) ...Details: Morpheus E7: 0.12 M ethylene glycols (0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol), 0.1 M sodium HEPES/MOPS pH 7.5, 50 % (v/v) of a mixture of glycerol (40 % v/v) and PEG 4000 (20 % w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999977 Å / Relative weight: 1
ReflectionResolution: 2.01→49.051 Å / Num. obs: 145908 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.18 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.162 / Net I/σ(I): 6.32
Reflection shellResolution: 2.01→2.13 Å / Mean I/σ(I) obs: 0.45 / Num. unique obs: 22740 / CC1/2: 0.178 / Rrim(I) all: 0.217 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
PHENIX1.19_4085refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5OMF

5omf


Resolution: 2.01→46.28 Å / SU ML: 0.3408 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 6950 4.82 %
Rwork0.2001 137334 -
obs0.2018 144284 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.51 Å2
Refinement stepCycle: LAST / Resolution: 2.01→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6209 668 56 277 7210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01467178
X-RAY DIFFRACTIONf_angle_d1.27889825
X-RAY DIFFRACTIONf_chiral_restr0.0651054
X-RAY DIFFRACTIONf_plane_restr0.00941155
X-RAY DIFFRACTIONf_dihedral_angle_d17.00182812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.39091680.40443122X-RAY DIFFRACTION66.33
2.03-2.050.38252190.37984072X-RAY DIFFRACTION86.99
2.05-2.080.40032180.3734325X-RAY DIFFRACTION93.4
2.08-2.10.35522550.35894607X-RAY DIFFRACTION97.93
2.1-2.130.36622350.34164661X-RAY DIFFRACTION99.57
2.13-2.160.38662110.32834691X-RAY DIFFRACTION99.76
2.16-2.190.35682360.31984597X-RAY DIFFRACTION99.83
2.19-2.220.3352200.31114714X-RAY DIFFRACTION99.78
2.22-2.260.32552440.30644642X-RAY DIFFRACTION99.82
2.26-2.30.33172540.2854680X-RAY DIFFRACTION99.68
2.3-2.330.3342070.28634658X-RAY DIFFRACTION99.73
2.33-2.380.29672190.26774703X-RAY DIFFRACTION99.72
2.38-2.420.29432200.26314663X-RAY DIFFRACTION99.82
2.42-2.470.27682430.25044662X-RAY DIFFRACTION99.65
2.47-2.530.3122670.23954592X-RAY DIFFRACTION99.63
2.53-2.590.26252320.23754706X-RAY DIFFRACTION99.68
2.59-2.650.31152290.22924647X-RAY DIFFRACTION99.35
2.65-2.720.27412460.23054630X-RAY DIFFRACTION99.39
2.72-2.80.26632300.22074651X-RAY DIFFRACTION99.88
2.8-2.890.26062370.22284675X-RAY DIFFRACTION99.86
2.89-30.26432300.19634680X-RAY DIFFRACTION99.86
3-3.120.2542140.1924682X-RAY DIFFRACTION99.92
3.12-3.260.2112490.18074701X-RAY DIFFRACTION99.76
3.26-3.430.20742360.17854624X-RAY DIFFRACTION99.73
3.43-3.640.23632530.17314622X-RAY DIFFRACTION99.59
3.64-3.920.19442340.15524687X-RAY DIFFRACTION99.39
3.92-4.320.16252240.14544659X-RAY DIFFRACTION99.84
4.32-4.940.16212230.13514686X-RAY DIFFRACTION99.94
4.94-6.220.21232410.16334662X-RAY DIFFRACTION99.88
6.23-46.280.18112560.16944633X-RAY DIFFRACTION99.25
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)
12.09094420327-0.0263214422-1.134510602930.6143857033780.3828173037672.150202147440.0505050522182-0.03847709002030.189471643683-0.006573990695230.03380454267750.00688236130149-0.0162862754250.0871004833089-0.09271072184240.240735529487-0.0110832968314-0.04780942960880.2647933759330.04073724996840.289445453973-16.519254915439.9140209874-7.05959550117
25.40778617210.1114225721460.1790082381922.394994914740.8595048701462.085813499660.06579158456620.345584474984-0.666249870968-0.0452781449248-0.01882567926440.08931965866050.2431810369320.0386362341805-0.0381371680880.335500938693-0.0113442198606-0.003670224819170.3465529586560.03915794403410.316052348538-8.9935988280628.1653232919-23.6895906442
31.455789528680.3624668914880.3276432478840.5376166602080.0918678805060.413684770924-0.03828422674920.133542479373-0.0118549700903-0.04130794828390.02524815426410.04316542897150.01906466121580.01349805269610.01768207561270.2309947916530.0200377654518-0.009161471764820.2606240206760.005583108364270.244328996631-39.927064246324.820143816-16.3024136961
43.24795677368-1.062869450810.2235378906971.14069737718-0.01603381392150.9548888529840.06547758978370.37233026276-0.259566305974-0.171124013315-0.0702681168667-0.1714206202370.141589986820.207565375818-0.0004306597968090.3584153946660.00106735056930.0440932513450.365641095971-0.0234732379780.452565903556-28.17698438323.63734872124-30.4716560187
58.553187515273.390906537823.924007772761.836580086982.34284932016.025361108010.85764035234-0.373680426679-1.763104352570.295752980096-0.205668503756-0.7664037077261.138857683090.698873768361-0.7062269742330.6151265853990.105459507494-0.04540170683420.665191496045-0.03044172065510.818271529166-15.261918317130.7191281076-1.97622002016
62.75591631556-0.239973015311-0.8631218391449.201872375261.077713601910.4057439196350.0984021855868-0.17701840145-0.4647447104110.448764541193-0.124167928621-0.506222706150.1104868878260.1553568483780.02949661290630.3314352522230.0294647316943-0.03119389146750.371801856970.1336808762220.338949448899-28.9501692134.38651632349-12.3512668001
74.75001067851-2.680191620452.493007599018.69377745072-4.568164751054.08836308785-0.134975061849-0.498205123682-0.5433028877240.1055803614210.146238800017-0.0194934948530.286511319424-0.05427867379330.03741056621640.3939176515520.06205830095840.06048207434240.355256616843-0.037982591140.385011678928-30.6982698114-0.894793661657-15.8408902387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 214 )AA1 - 2141 - 214
22chain 'A' and (resid 215 through 304 )AA215 - 304215 - 304
33chain 'A' and (resid 305 through 552 )AA305 - 552305 - 552
44chain 'A' and (resid 553 through 756 )AA553 - 756553 - 756
55chain 'T' and (resid 1 through 5 )TB1 - 5
66chain 'T' and (resid 6 through 21 )TB6 - 21
77chain 'P' and (resid 1 through 12 )PC1 - 12

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