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

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Basic information

Entry
Database: PDB / ID: 7omg
TitleCrystal structure of KOD DNA Polymerase in a ternary complex with an Uracil containing template
Components
  • DNA polymerase
  • Primer
  • Template
KeywordsREPLICATION / ternary complex / DNA polymerase / uracil
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: 2.1 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 22, 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 6, 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)100,92712
Polymers100,0933
Non-polymers8349
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-74 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.403, 147.138, 71.129
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

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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: D141A,E143A
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: 6431.130 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 , 7 types, 97 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.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Morpheus A3: 0.06MDivalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate) 0.1M Buffer System 1 (1 M MES/Imidazol pH 6.5) 30% v/vPrecipitant Mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 2.1→49.026 Å / Num. obs: 66516 / % possible obs: 99.2 % / Redundancy: 9.8 % / Biso Wilson estimate: 53.96 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.142 / Net I/σ(I): 11.49
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 0.39 / Num. unique obs: 10239 / CC1/2: 0.157 / Rrim(I) all: 0.4266

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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: 2.1→46.25 Å / SU ML: 0.494 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 35.0045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 6061 4.77 %
Rwork0.2098 120902 -
obs0.2116 66516 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 648 44 88 6906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00877025
X-RAY DIFFRACTIONf_angle_d1.02369615
X-RAY DIFFRACTIONf_chiral_restr0.05471034
X-RAY DIFFRACTIONf_plane_restr0.00841116
X-RAY DIFFRACTIONf_dihedral_angle_d18.49752723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.48351480.4643511X-RAY DIFFRACTION86.09
2.12-2.150.51082050.44963778X-RAY DIFFRACTION93.39
2.15-2.170.46131820.44173963X-RAY DIFFRACTION96.49
2.17-2.20.37911880.41334010X-RAY DIFFRACTION98.66
2.2-2.230.37222220.38564051X-RAY DIFFRACTION99.16
2.23-2.260.45661940.47163891X-RAY DIFFRACTION96.12
2.26-2.290.44142080.38624078X-RAY DIFFRACTION99.91
2.29-2.330.33521780.35454084X-RAY DIFFRACTION99.91
2.33-2.360.34951880.33344151X-RAY DIFFRACTION99.98
2.36-2.40.37871950.31614067X-RAY DIFFRACTION99.98
2.4-2.440.32012040.30994069X-RAY DIFFRACTION100
2.44-2.490.35092250.29644003X-RAY DIFFRACTION100
2.49-2.540.30742370.28574084X-RAY DIFFRACTION99.98
2.54-2.590.281850.27964062X-RAY DIFFRACTION99.98
2.59-2.650.32122020.26984088X-RAY DIFFRACTION99.84
2.65-2.710.34552180.28074040X-RAY DIFFRACTION99.98
2.71-2.770.31721940.26164083X-RAY DIFFRACTION99.86
2.77-2.850.28512070.26014076X-RAY DIFFRACTION99.84
2.85-2.930.34452210.2584035X-RAY DIFFRACTION99.95
2.93-3.030.24791830.24844098X-RAY DIFFRACTION99.98
3.03-3.140.29061890.23464080X-RAY DIFFRACTION100
3.14-3.260.25262270.21674079X-RAY DIFFRACTION100
3.26-3.410.22271970.20624092X-RAY DIFFRACTION100
3.41-3.590.25832300.19614013X-RAY DIFFRACTION100
3.59-3.810.23862170.18694065X-RAY DIFFRACTION100
3.81-4.110.23972000.16624044X-RAY DIFFRACTION99.69
4.11-4.520.1751790.14614125X-RAY DIFFRACTION99.91
4.52-5.180.18652100.14494061X-RAY DIFFRACTION100
5.18-6.520.19922150.17154077X-RAY DIFFRACTION99.95
6.52-46.250.18462130.15474044X-RAY DIFFRACTION99.6
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)
13.609285664280.256872817798-1.049122202351.208472779290.1992426228492.44984571432-0.03143542990220.178276090890.363296146607-0.08151901426170.061414724477-0.03850928874410.0849099287594-0.0373339232953-0.05676652757210.371714120074-0.0596953260293-0.08303471069930.3636313443110.01679815596790.431662665969-16.469797770539.8357308744-7.00527232584
24.97991093185-3.431493923142.422019201565.705325279051.227390154334.337577687550.172746020764-0.160443548359-0.08628940711420.0702234593186-0.008947396072180.1124683419270.308771908016-0.159378680139-0.1313034775040.495788069032-0.1283387896770.02183718304750.6639106733750.00593912745060.50850468718-5.0394737586833.9769134109-14.218159915
34.25370456719-0.141197827586-2.067007178531.242642642930.0751451228393.20623094127-0.2598799063171.03254070756-0.526399746122-0.5371170772510.105069238544-0.1280776085790.2217939385490.2294777717380.1667204612970.581356591992-0.1384414720470.006180295203360.896166467637-0.1411151041930.531416176454-17.311763152528.8537682142-25.4959879885
43.279009388180.3701039316321.648966994642.075595004270.4107171650522.96473147415-0.04286053242870.328862086023-0.247981762499-0.198139086817-0.06945563379180.3228852872170.033076365703-0.1033663460730.1335987105520.3357448718340.0198741243836-0.02670619777950.363944871203-0.09162427054640.467855725734-46.801186453621.6809064363-16.339934927
52.74518206542-0.9365750035930.4678247082032.14519925244-0.06618196123571.675092761290.06962908830060.634646866911-0.381646796576-0.480054310113-0.263579158347-0.3779392971110.3945179192550.4101322674390.1805554441780.6318484912590.09160890217650.1219572735670.595894722593-0.07966073973360.71038745763-24.9917510052.6380292168-30.071847096
66.349899036955.724675078335.263200673975.204957577034.653342179544.612943051710.829339656771.9379789717-2.03437602658-1.0917088496-0.09944708635-2.086313723140.854347968661.21347119145-0.6425066060320.842605177250.1815078773690.01741020497020.854966048924-0.223216045960.955886565229-18.812930894730.5844819176-1.04197351619
71.34004416021-2.327713566040.6426190487544.92542968717-0.3320974745340.7185520030040.172403480549-0.12770511012-0.616762400294-0.0611636112305-0.185390463286-0.3021071822840.538036804550.1856532163470.007521538382330.6871702201960.03891222738210.06864451315230.5330994560030.04969123307260.954034046819-30.42857272321.47067726839-14.1051342107
80.508939987706-0.7446906394090.4915051380976.90587934599-0.2824405991150.6676100759830.0352524665457-0.144191186676-0.6704698253430.985589454734-0.130798878913-0.3388276113660.00933111110270.05796024667760.09411009389670.6956289703950.0710820223440.03817205361390.5761956805040.02643177036410.99382861282-30.9488225924-1.11500691502-16.0589424204
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 255 )AA215 - 255215 - 255
33chain 'A' and (resid 256 through 363 )AA256 - 363256 - 363
44chain 'A' and (resid 364 through 570 )AA364 - 570364 - 570
55chain 'A' and (resid 571 through 747 )AA571 - 747571 - 747
66chain 'T' and (resid 2 through 7 )TC - E2 - 7
77chain 'T' and (resid 8 through 21 )TE8 - 21
88chain 'P' and (resid 1 through 12 )PF1 - 12

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