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- PDB-8xk9: ternary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy ... -

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Basic information

Entry
Database: PDB / ID: 8xk9
Titleternary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide
Components
  • DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
  • DNA polymerase I, thermostable
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: 2.4 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
B: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
C: DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3')
A: DNA polymerase I, thermostable
E: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
F: DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3')
D: DNA polymerase I, thermostable
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,39118
Polymers138,7696
Non-polymers1,62212
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.986, 105.986, 191.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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DNA chain , 2 types, 4 molecules BECF

#1: DNA chain DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')


Mass: 3617.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3')


Mass: 4970.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AD

#3: Protein DNA polymerase I, thermostable / Taq polymerase 1


Mass: 60796.840 Da / Num. of mol.: 2
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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Non-polymers , 5 types, 549 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-A1LWE / [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 537.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 10% propanol, and 20% PEG 4000

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 82487 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.054 / Rrim(I) all: 0.142 / Χ2: 1.616 / Net I/σ(I): 5.8 / Num. measured all: 561436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.446.40.61941020.8670.9640.2630.6730.562100
2.44-2.496.90.56341330.8960.9720.230.6090.571100
2.49-2.536.90.4840900.9210.9790.1970.520.618100
2.53-2.596.90.42941760.930.9820.1750.4640.642100
2.59-2.646.90.39340900.940.9840.1610.4250.672100
2.64-2.76.90.33840790.9480.9870.1380.3650.74100
2.7-2.776.90.30941170.9570.9890.1260.3340.784100
2.77-2.856.90.2741360.9650.9910.110.2920.864100
2.85-2.9370.23541350.9740.9930.0950.2540.967100
2.93-3.026.90.20940860.9730.9930.0860.2261.151100
3.02-3.136.80.18441430.9770.9940.0760.21.337100
3.13-3.266.70.16440930.9820.9950.0680.1771.729100
3.26-3.416.10.14541060.9840.9960.0640.1582.06799.8
3.41-3.586.20.13641510.9850.9960.0590.1492.57100
3.58-3.817.30.12641240.9880.9970.050.1362.798100
3.81-4.17.30.11841170.9910.9980.0470.1273.099100
4.1-4.527.20.10841270.9910.9980.0430.1163.24599.9
4.52-5.1770.09841570.9930.9980.040.1062.84899.9
5.17-6.516.40.09341280.9920.9980.0390.1012.27699.8
6.51-506.60.08341970.9930.9980.0350.092.67499.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.1 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.753 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21791 4146 5 %RANDOM
Rwork0.1774 ---
obs0.17934 78293 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20 Å2
2---0.18 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.4→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8513 1138 95 537 10283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210128
X-RAY DIFFRACTIONr_bond_other_d0.0020.0168878
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.66813948
X-RAY DIFFRACTIONr_angle_other_deg0.4381.54820650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18451085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.09610109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.613101519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.21533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022001
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_it3.1994.5554325
X-RAY DIFFRACTIONr_mcbond_other3.1954.5554325
X-RAY DIFFRACTIONr_mcangle_it4.6696.8355412
X-RAY DIFFRACTIONr_mcangle_other4.6696.8355413
X-RAY DIFFRACTIONr_scbond_it4.2075.0715803
X-RAY DIFFRACTIONr_scbond_other4.1995.0655796
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3827.4818524
X-RAY DIFFRACTIONr_long_range_B_refined8.20157.66111750
X-RAY DIFFRACTIONr_long_range_B_other8.20157.66811751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å
RfactorNum. reflection% reflection
Rfree0.255 328 -
Rwork0.243 5729 -
obs--99.33 %

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