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- PDB-7om3: Crystal structure of KOD DNA Polymerase in a binary complex with ... -

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Basic information

Entry
Database: PDB / ID: 7om3
TitleCrystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing template
Components
  • 21nt Template
  • DNA polymerase,DNA polymerase,DNA polymerase
  • Primer
KeywordsREPLICATION / Hypoxanthine / binary 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
BROMIDE ION / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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,DNA polymerase,DNA polymerase
T: 21nt Template
P: Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,66110
Polymers100,1173
Non-polymers5447
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-6 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.356, 142.936, 65.582
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-1335-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase,DNA polymerase,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 / Plasmid: pET24a / 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 21nt Template


Mass: 6455.155 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, 389 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
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: 1.0000089622351 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: 1.0000089622351 Å / Relative weight: 1
ReflectionResolution: 1.91→48.32 Å / Num. obs: 147921 / % possible obs: 93.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 35.88 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.148 / Net I/σ(I): 7.39
Reflection shellResolution: 1.91→2.03 Å / Redundancy: 2.2 % / Num. unique obs: 16579 / CC1/2: 0.185 / % possible all: 64.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
PHENIX1.19_4085refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8Z

4k8z


Resolution: 1.92→44.45 Å / SU ML: 0.3079 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3061
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 3691 2.55 %
Rwork0.1829 141263 -
obs0.1841 144954 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 667 27 382 7315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01237155
X-RAY DIFFRACTIONf_angle_d1.2149780
X-RAY DIFFRACTIONf_chiral_restr0.06141047
X-RAY DIFFRACTIONf_plane_restr0.01181139
X-RAY DIFFRACTIONf_dihedral_angle_d18.22372788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.3812250.35821193X-RAY DIFFRACTION20.47
1.95-1.970.42880.37233357X-RAY DIFFRACTION56.89
1.97-20.39731120.35474283X-RAY DIFFRACTION72.9
2-2.030.35951210.35014669X-RAY DIFFRACTION79.61
2.03-2.060.33891300.34945102X-RAY DIFFRACTION85.83
2.06-2.10.36151410.32815424X-RAY DIFFRACTION92.63
2.1-2.130.38761460.31235663X-RAY DIFFRACTION96.14
2.13-2.170.33581500.28995804X-RAY DIFFRACTION98.82
2.17-2.210.34471550.27415864X-RAY DIFFRACTION99.49
2.21-2.260.33021520.25785895X-RAY DIFFRACTION99.93
2.26-2.310.26291580.23565867X-RAY DIFFRACTION99.97
2.31-2.360.27321530.23265879X-RAY DIFFRACTION99.98
2.36-2.420.26611600.21985940X-RAY DIFFRACTION99.98
2.42-2.490.26891510.21415798X-RAY DIFFRACTION99.92
2.49-2.560.27381540.2115864X-RAY DIFFRACTION99.93
2.56-2.640.26821530.20815923X-RAY DIFFRACTION99.95
2.64-2.740.26921560.19655897X-RAY DIFFRACTION99.74
2.74-2.850.24961540.1875868X-RAY DIFFRACTION99.9
2.85-2.970.22721530.18115878X-RAY DIFFRACTION99.93
2.97-3.130.26261530.18625843X-RAY DIFFRACTION99.95
3.13-3.330.20621500.1785869X-RAY DIFFRACTION99.87
3.33-3.580.20631540.15325866X-RAY DIFFRACTION99.97
3.58-3.950.20761580.14355909X-RAY DIFFRACTION99.95
3.95-4.520.16991500.12245861X-RAY DIFFRACTION99.88
4.52-5.690.13951550.12535900X-RAY DIFFRACTION99.98
5.69-44.450.25131590.15985847X-RAY DIFFRACTION99.59
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)
12.479542436380.355973251505-1.428491607480.654665370553-0.6253412246212.38031410335-0.008227957597080.2300862046350.133623384064-0.07552156867680.01928290454540.00183459555285-0.0326276438497-0.106291142446-0.02582432941630.2019871281520.0137904557789-0.04500562294430.194090083233-0.00355488550560.23125609924116.406686417735.19200139075.9874836585
23.754939333260.301303161445-0.2463330537482.76006140623-1.17846215641.66744746061-0.07581176000890.0737173142943-0.310493192035-0.2037883826190.0256215818395-0.06572667991390.255825239735-0.1259063271680.06114472690960.273707358066-0.002659684641290.02912363292650.254967143189-0.06744651110790.21857348625610.070037518322.988713192321.6394833972
30.751108226973-0.09886094912990.1026655326220.507585991866-0.138330558260.367027495570.000652870295963-0.10150253672-0.04753630349220.0177131308208-0.0373834221177-0.1510876935020.04816813015020.08934785962820.03303837253390.259731096475-0.01192832743330.001298959424570.3139211116120.03732913761950.31336278115641.904527585124.836994471616.2506817779
43.788912508881.61198514392-0.07487869927221.72506051973-0.02316207712470.9224337910650.160029747481-0.483984722088-0.3874621893750.252599315095-0.19392531813-0.01375253882690.104186671909-0.04358995969090.04187293306780.3136811065470.01979340463840.0407414906730.3269856153040.04819893850150.40530070286932.43049367752.9462605544531.9154929998
55.2672797834-3.427586666873.945899751712.81339847628-1.949656291333.624875379850.0858594976966-0.285793358896-2.00292939670.04599183934130.4735884502650.6155265363431.316872575-0.70142494716-0.6958687276920.471450418665-0.0700945446343-0.02336931799680.5026733075350.06723081036060.52307910312117.774036938729.9814407805-2.01368978178
62.227159340071.89037644721-1.144916098333.723162296721.230843372223.57605836117-0.04636988581030.371924381635-0.126591934819-0.0398369990583-0.06919571015710.5280000675530.259783423128-0.245736873540.06612705375410.2577375000360.03346194006280.01562147057210.3388151484690.008758810014040.54960390672233.16856470241.6841345051814.3191926687
71.534657388770.7654447714881.047675568328.609639442031.785818001683.30678229110.119272667480.16993351824-0.883295892394-0.795369913338-0.100651961076-1.08956544280.210206698165-0.0117933384763-0.03618563540130.34003639706-0.01745078816830.1403211280820.421530199943-0.02776220916490.74439865500433.7797703409-3.9092077934516.550502021
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 759 )AA553 - 759553 - 759
55chain 'T' and (resid 1 through 6 )TC - E1 - 6
66chain 'T' and (resid 7 through 21 )TE7 - 21
77chain 'P' and (resid 1 through 11 )PF1 - 11

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