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- PDB-6rp0: The crystal structure of a complex between the LlFpg protein, a T... -

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Basic information

Entry
Database: PDB / ID: 6rp0
TitleThe crystal structure of a complex between the LlFpg protein, a THF-DNA and an inhibitor
Components
  • DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)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 / DNA glycosylase complex / inhibitor
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / 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
2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one / DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsCoste, F. / Goffinont, S. / Castaing, B.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights.
Authors: Rieux, C. / Goffinont, S. / Coste, F. / Tber, Z. / Cros, J. / Roy, V. / Guerin, M. / Gaudon, V. / Bourg, S. / Biela, A. / Aucagne, V. / Agrofoglio, L. / Garnier, N. / Castaing, B.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
B: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)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')
F: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8746
Polymers43,5814
Non-polymers2922
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-30 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.180, 92.180, 139.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE


Mass: 31116.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A165FVI1, UniProt: P42371*PLUS

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DNA chain , 2 types, 3 molecules BFC

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


Mass: 4054.614 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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)

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Non-polymers , 3 types, 128 molecules

#4: Chemical ChemComp-5JL / 2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one


Mass: 200.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4OS2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, CITRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.25→47.66 Å / Num. obs: 29044 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 2.25→2.37 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4126 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PM5

1pm5


Resolution: 2.25→41.57 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 2687 4.96 %
Rwork0.1635 51539 -
obs0.1654 54226 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.73 Å2 / Biso mean: 53.3085 Å2 / Biso min: 27.9 Å2
Refinement stepCycle: final / Resolution: 2.25→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 696 18 126 2931
Biso mean--46.55 50.76 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082923
X-RAY DIFFRACTIONf_angle_d1.1814081
X-RAY DIFFRACTIONf_chiral_restr0.044462
X-RAY DIFFRACTIONf_plane_restr0.005398
X-RAY DIFFRACTIONf_dihedral_angle_d20.1371145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2501-2.2910.32411220.29042744286699
2.291-2.3350.29521270.28142678280599
2.335-2.38270.32061280.2662726285499
2.3827-2.43450.31341570.24832703286099
2.4345-2.49110.28291320.242727542886100
2.4911-2.55340.30161490.23622691284099
2.5534-2.62240.3281410.2442730287199
2.6224-2.69960.26211240.2252738286299
2.6996-2.78670.251680.22482678284699
2.7867-2.88630.30281480.21322693284199
2.8863-3.00180.22981390.207926972836100
3.0018-3.13840.22751570.18527092866100
3.1384-3.30380.2291360.169927282864100
3.3038-3.51070.16641500.137127272877100
3.5107-3.78160.18691510.131226962847100
3.7816-4.16180.16421390.12222724286399
4.1618-4.76330.11711320.101927392871100
4.7633-5.99840.16041390.12892691283099
5.9984-41.57740.16551480.14742693284199
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)
16.01492.32-2.22616.1931-2.6994.361-0.14820.2893-0.5695-0.32210.0419-0.60260.31220.14760.15930.40210.05730.04710.3597-0.00570.531-1.12853.1437-16.272
21.3860.8426-1.29337.43422.5664.7155-0.0972-0.2986-0.01410.55170.10160.3160.3195-0.1933-0.00650.27150.0037-0.03820.4830.06540.3716-16.09524.2714-5.7795
32.0892-0.2659-1.97231.9208-0.82123.6312-0.19220.265-0.3851-0.15780.07740.26950.3611-0.61610.13650.2413-0.0796-0.05310.37970.0110.338-15.94935.472-15.9468
40.3236-0.5669-0.42424.5217-2.78144.21460.1507-0.3231-0.110.696-0.2123-0.0408-0.10290.45690.08870.3561-0.0328-0.07250.4360.04420.3799-5.13577.8115-2.6287
51.6081.1577-0.66761.9046-0.84842.7374-0.16670.1389-0.2508-0.11030.1324-0.13880.3335-0.1974-0.00780.26420.01-0.05190.401-0.00650.3578-9.78069.8151-17.2986
64.6991.0136-0.35684.58440.72876.0348-0.16660.22980.0702-0.42260.1446-0.2142-0.47450.22350.05210.2735-0.06110.01350.34780.01380.34556.377822.9669-30.7765
73.33932.1596-2.76096.8505-5.70417.964-0.22310.3495-0.6816-0.6447-0.2877-0.55890.76430.55890.56130.30340.00780.09450.5078-0.07640.560510.163412.5429-31.1781
85.6076.6148-0.13328.0452-0.18140.01280.3872-0.7824-1.10360.259-0.7903-1.18480.12760.41260.46250.426-0.0157-0.0770.76540.1680.871911.43399.5659-13.9538
92.25221.57940.47933.3022-0.9026.1514-0.24220.2235-0.1565-0.3023-0.1172-0.9783-0.33161.06520.27370.3723-0.1456-0.0210.62320.04010.684618.156625.8904-20.0792
103.12090.60890.13171.91430.20923.80090.2007-0.25150.3593-0.191-0.15580.2267-0.8274-0.0972-0.02910.49860.0034-0.0330.4917-0.03210.4674-2.715431.241-11.7905
113.44934.1041-5.01125.156-6.12957.5210.7759-0.0822-0.08230.0542-0.37590.7877-0.17490.4293-0.18370.66520.1426-0.09050.52870.03750.4688-5.093933.9149-19.455
125.43815.32613.32745.30382.68525.6059-0.2958-1.0964-0.11860.33620.0425-1.1647-0.4716-0.00320.18920.4709-0.0425-0.11230.4732-0.05150.57942.550525.55450.184
136.58863.40483.58247.79341.60752.354-1.01951.1483-1.99090.71841.2571-0.1197-1.60690.1159-0.23391.0551-0.1935-0.21931.2819-0.03741.10062.759827.8376.4436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )A1 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 32 )A18 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 72 )A33 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 91 )A73 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 141 )A92 - 141
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 193 )A142 - 193
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 213 )A194 - 213
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 239 )A214 - 239
9X-RAY DIFFRACTION9chain 'A' and (resid 240 through 271 )A240 - 271
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 14 )B1 - 14
11X-RAY DIFFRACTION11chain 'C' and (resid 15 through 22 )C15 - 22
12X-RAY DIFFRACTION12chain 'C' and (resid 23 through 28 )C23 - 28
13X-RAY DIFFRACTION13chain 'E' and (resid 6 through 12 )E6 - 12

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