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- PDB-8xk7: binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy n... -

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Basic information

Entry
Database: PDB / ID: 8xk7
Titlebinary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide
Components
  • DNA polymerase I, thermostable
  • DNA(5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP*OMG)-3')
  • DNA(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*CP*OMG)-3')
KeywordsDNA BINDING PROTEIN / DNA polymerase
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 / Helix-hairpin-helix motif, class 2 ...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 / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWen, C. / Liu, H. / Yang, L. / Gong, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement.
Authors: Wen, C. / Wang, G. / Yang, L. / Chen, T. / Liu, H. / Gong, W.
History
DepositionDec 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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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: DNA(5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP*OMG)-3')
C: DNA(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*CP*OMG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3269
Polymers71,7423
Non-polymers5846
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-55 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.610, 65.628, 107.378
Angle α, β, γ (deg.)90.00, 103.51, 90.00
Int Tables number4
Space group name H-MP1211

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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: 62465.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA(5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP*OMG)-3')


Mass: 5283.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*CP*OMG)-3')


Mass: 3992.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 352 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, and 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 55909 / % possible obs: 98.8 % / Redundancy: 6.1 % / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.06 / Rrim(I) all: 0.148 / Χ2: 1.29 / Net I/σ(I): 4.3 / Num. measured all: 343365
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.036.30.58627770.9150.9780.2550.640.54199.7
2.03-2.076.30.53728240.9270.9810.2330.5860.57699.8
2.07-2.116.30.47527890.950.9870.2060.5190.59499.5
2.11-2.156.20.39427770.9550.9880.1720.4310.62499.2
2.15-2.26.20.35728090.9720.9930.1560.390.63799
2.2-2.256.20.30827720.970.9920.1350.3370.7298.8
2.25-2.316.10.28827320.9630.990.1270.3150.80498
2.31-2.375.70.25727430.9630.990.1190.2840.85796.3
2.37-2.445.80.23427350.9690.9920.1060.2570.93797.9
2.44-2.526.50.22228320.9750.9940.0950.2411.06599.8
2.52-2.616.40.20827850.9750.9940.0890.2261.11499.8
2.61-2.716.40.19128240.9790.9950.0820.2081.26399.8
2.71-2.846.30.17328270.9790.9950.0750.1891.32199.6
2.84-2.996.30.15728200.9820.9950.0690.1711.46399.4
2.99-3.176.10.14227730.9850.9960.0630.1561.799.2
3.17-3.425.70.12827660.9850.9960.0590.1412.07396.8
3.42-3.7660.11527870.9870.9970.0520.1272.25398.6
3.76-4.316.30.10928420.9880.9970.0480.122.44399.5
4.31-5.436.10.10628390.9880.9970.0470.1162.3799.3
5.43-505.60.10628560.9890.9970.0490.1172.6196.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.568 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2832 5.1 %RANDOM
Rwork0.19151 ---
obs0.19347 53014 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.354 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å2-0 Å2-1.33 Å2
2--3.74 Å2-0 Å2
3----4.27 Å2
Refinement stepCycle: 1 / Resolution: 2→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 619 32 346 5312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125146
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164516
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.6677099
X-RAY DIFFRACTIONr_angle_other_deg0.3861.54810502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.9591055
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28610768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2823.6952193
X-RAY DIFFRACTIONr_mcbond_other2.2823.6952193
X-RAY DIFFRACTIONr_mcangle_it3.2935.5332743
X-RAY DIFFRACTIONr_mcangle_other3.2945.5362744
X-RAY DIFFRACTIONr_scbond_it2.8434.132953
X-RAY DIFFRACTIONr_scbond_other2.8424.1312954
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3266.0764357
X-RAY DIFFRACTIONr_long_range_B_refined5.95746.2755989
X-RAY DIFFRACTIONr_long_range_B_other5.95746.285990
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 224 -
Rwork0.283 3894 -
obs--99.13 %

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