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- PDB-6fl1: Crystal structure of the complex between the Lactococcus lactis F... -

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Basic information

Entry
Database: PDB / ID: 6fl1
TitleCrystal structure of the complex between the Lactococcus lactis FPG mutant T221P and a Fapy-dG containing DNA
Components
  • DNA (5'-D(*CP*TP*CP*TP*TP*TP(FOX)P*TP*TP*TP*CP*TP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
  • Formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE / PROTEIN-DNA COMPLEX / GLYCOSYLASE / FAPY LESION
Function / homology
Function and homology information


oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-formamidopyrimidine glycosylase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins ...Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCoste, F. / Castaing, B. / Ober, M. / Carell, T.
CitationJournal: To Be Published
Title: Crystal structure of the complex between the Lactococcus lactis FPG mutant T221P and a Fapy-dG containing DNA
Authors: Coste, F. / Castaing, B. / Ober, M. / Carell, T.
History
DepositionJan 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*TP*CP*TP*TP*TP(FOX)P*TP*TP*TP*CP*TP*CP*G)-3')
C: DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
A: Formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7534
Polymers39,6883
Non-polymers651
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-20 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.369, 91.369, 141.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-5218-

HOH

21A-5396-

HOH

31A-5423-

HOH

41A-5440-

HOH

51A-5492-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*TP*CP*TP*TP*TP(FOX)P*TP*TP*TP*CP*TP*CP*G)-3')


Mass: 4219.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')


Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Formamidopyrimidine-DNA glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase MutM / AP lyase MutM


Mass: 31112.229 Da / Num. of mol.: 1 / Mutation: T221P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Gene: mutM, fpg, NCDO763_0992 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A165FVI1, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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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: 3.73 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2013 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.6→47.74 Å / Num. obs: 78211 / % possible obs: 98.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 10201 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XC8

1xc8


Resolution: 1.6→47.735 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 17.73
RfactorNum. reflection% reflection
Rfree0.1783 7449 5.04 %
Rwork0.1631 --
obs0.1639 78143 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→47.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 569 1 459 3181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072878
X-RAY DIFFRACTIONf_angle_d0.9893997
X-RAY DIFFRACTIONf_dihedral_angle_d11.7022214
X-RAY DIFFRACTIONf_chiral_restr0.061450
X-RAY DIFFRACTIONf_plane_restr0.006412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6004-1.61860.29931960.2483612X-RAY DIFFRACTION76
1.6186-1.63770.24081930.24133999X-RAY DIFFRACTION82
1.6377-1.65760.22812280.23234219X-RAY DIFFRACTION89
1.6576-1.67860.24472410.22184513X-RAY DIFFRACTION95
1.6786-1.70070.22011980.19534833X-RAY DIFFRACTION99
1.7007-1.7240.22642130.19434810X-RAY DIFFRACTION100
1.724-1.74860.19982380.19164746X-RAY DIFFRACTION100
1.7486-1.77470.2562380.18624818X-RAY DIFFRACTION100
1.7747-1.80250.18842230.18264795X-RAY DIFFRACTION100
1.8025-1.8320.20432370.1914777X-RAY DIFFRACTION100
1.832-1.86360.21222620.19074777X-RAY DIFFRACTION100
1.8636-1.89750.20752650.17684768X-RAY DIFFRACTION100
1.8975-1.9340.18872900.16374719X-RAY DIFFRACTION100
1.934-1.97350.18352710.15874794X-RAY DIFFRACTION100
1.9735-2.01640.1642590.16844720X-RAY DIFFRACTION100
2.0164-2.06330.19713060.17024748X-RAY DIFFRACTION100
2.0633-2.11490.19772480.1684763X-RAY DIFFRACTION100
2.1149-2.17210.18542410.15834820X-RAY DIFFRACTION100
2.1721-2.2360.16682880.15144731X-RAY DIFFRACTION100
2.236-2.30810.17042570.15844783X-RAY DIFFRACTION100
2.3081-2.39060.16382610.16144775X-RAY DIFFRACTION100
2.3906-2.48640.18872450.15994794X-RAY DIFFRACTION100
2.4864-2.59950.18352600.17224753X-RAY DIFFRACTION100
2.5995-2.73650.22662380.18194797X-RAY DIFFRACTION100
2.7365-2.9080.16612300.1854793X-RAY DIFFRACTION100
2.908-3.13250.22182870.18044765X-RAY DIFFRACTION100
3.1325-3.44760.16092490.15544783X-RAY DIFFRACTION100
3.4476-3.94630.14492540.13594778X-RAY DIFFRACTION100
3.9463-4.97110.1362920.11914754X-RAY DIFFRACTION100
4.9711-47.75620.1592410.15684715X-RAY DIFFRACTION98
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)
10.21050.0591-0.03030.43780.30340.230.04620.03320.1330.18480.0089-0.169-0.04840.36370.00030.2260.0041-0.0530.25440.00130.203930.03642.8265165.3434
20.3233-0.12890.19820.1376-0.09640.1307-0.0759-0.19050.0344-0.04610.0213-0.11590.18710.69580.03830.25440.05530.00610.33590.03010.19429.91562.4479165.802
31.11050.1674-0.32590.4898-0.06511.03720.05590.03170.03380.0329-0.03490.1343-0.0854-0.08360.01710.13510.01550.00020.07930.00620.13184.980110.9528165.066
40.4085-0.2739-0.24140.72660.38751.25970.01890.0484-0.0321-0.022-0.02390.03360.07520.0645-0.00260.13320.0043-0.01470.11050.00680.132115.6549-0.2885151.4987
50.03-0.0143-0.01690.0267-0.02980.0627-0.2452-0.3668-0.2670.7792-0.07940.3860.12110.0198-0.00160.467-0.00760.06940.25440.01190.30097.1657-9.1506165.8783
60.1235-0.186-0.20430.770.25530.4078-0.2319-0.2385-0.06030.30330.2294-0.0640.50330.49950.11960.36720.1422-0.00080.11160.02370.164824.4109-17.4244157.7417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'C' and (resid 15 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 234 )
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 271 )

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