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- PDB-6rno: Crystal structure of a complex between the LlFpg protein, a THF-D... -

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Basic information

Entry
Database: PDB / ID: 6rno
TitleCrystal 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 glycosylaseDNA-formamidopyrimidine glycosylase
KeywordsHYDROLASE / DNA glycosylase complex / inhibitor
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion 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. / 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 / 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
Chem-KBQ / 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 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,7865
Polymers39,5273
Non-polymers2592
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-21 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.423, 91.423, 140.276
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 / DNA-formamidopyrimidine glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase MutM / AP lyase MutM


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)
Gene: mutM, fpg, NCDO763_0992 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A165FVI1, UniProt: P42371*PLUS, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 2 types, 2 molecules DE

#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.: 1 / 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, 77 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KBQ / 2-sulfanylidene-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one


Mass: 167.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N3OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.76 Å3/Da / Density % sol: 67.25 %
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→47.53 Å / Num. obs: 28957 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 52.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.3
Reflection shellResolution: 2.25→2.37 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4144

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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→47.535 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 2683 4.98 %
Rwork0.158 51199 -
obs0.16 53882 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.76 Å2 / Biso mean: 62.1 Å2 / Biso min: 32.22 Å2
Refinement stepCycle: final / Resolution: 2.25→47.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 557 17 75 2746
Biso mean--56.07 54.44 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112789
X-RAY DIFFRACTIONf_angle_d1.2623874
X-RAY DIFFRACTIONf_chiral_restr0.053438
X-RAY DIFFRACTIONf_plane_restr0.005394
X-RAY DIFFRACTIONf_dihedral_angle_d20.231090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2501-2.2910.28471210.297827332854
2.291-2.3350.30021300.277927022832
2.335-2.38270.27771390.251826992838
2.3827-2.43450.27751600.235226872847
2.4345-2.49110.27591350.227626862821
2.4911-2.55340.33041500.239827102860
2.5534-2.62250.30221190.233726862805
2.6225-2.69960.251350.215127402875
2.6996-2.78680.23281600.20826402800
2.7868-2.88630.26051550.201127142869
2.8863-3.00190.24581430.202626562799
3.0019-3.13850.24091470.187727112858
3.1385-3.30390.19541310.161526962827
3.3039-3.51090.19611570.132826782835
3.5109-3.78180.16361460.129226842830
3.7818-4.16220.151440.120927062850
4.1622-4.7640.12771300.109526932823
4.764-6.00030.18411390.130626922831
6.0003-47.54530.18691420.153426862828
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)
13.50931.0049-0.96054.3230.05485.2245-0.12450.0991-0.2194-0.54420.0559-0.86640.27391.21860.01010.62240.04340.08740.74330.07210.6344-60.887188.3991151.5705
27.63651.07567.09554.9421-0.03946.8187-0.5707-0.5107-0.61860.53690.1455-0.4366-0.8521.40840.68620.63530.1292-0.06561.24040.21760.6574-58.069285.7054159.5385
36.17793.65770.17553.5235-1.82872.75810.17630.59771.3502-1.5125-0.1747-0.139-0.78470.80950.08190.8765-0.11970.17350.72010.17190.7126-66.49493.5914139.8754
43.53840.51771.14132.13780.98254.46310.1228-0.043-0.0259-0.0317-0.15930.31560.3193-0.3510.04060.4738-0.0131-0.00560.33660.03450.4218-86.616180.5635152.0438
51.99740.93460.771.7540.70782.71840.1528-0.04660.04670.1458-0.18570.20290.387-0.20460.00080.48080.00090.01960.30770.05550.44-82.066681.6858157.7823
66.69260.0074-0.73365.0241.44547.8240.1821-0.78920.03920.5714-0.0571-0.19160.21630.6807-0.17850.4444-0.0964-0.01650.4387-0.00830.4396-67.746994.1955174.8159
73.08360.90211.03464.20420.43493.8029-0.0378-0.21470.50020.3054-0.2359-0.0127-0.5340.23720.27730.5951-0.06970.02180.3734-0.0130.5545-73.0504101.1055168.9624
88.98748.93511.45028.92751.42410.3169-0.84070.57151.0235-1.41730.44491.0195-0.9863-0.18730.38451.01330.0022-0.1430.59380.09040.9079-81.8245102.7216153.4161
94.60161.29852.58968.516-2.78437.7432-0.2446-0.01851.00490.2894-0.17740.1058-1.42940.45730.37060.8041-0.2359-0.02990.52370.0830.7359-65.7096109.0711159.797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 14 )D1 - 14
2X-RAY DIFFRACTION2chain 'E' and (resid 15 through 22 )E15 - 22
3X-RAY DIFFRACTION3chain 'E' and (resid 23 through 28 )E23 - 28
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 91 )A1 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 141 )A92 - 141
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 162 )A142 - 162
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 213 )A163 - 213
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 239 )A214 - 239
9X-RAY DIFFRACTION9chain 'A' and (resid 240 through 271 )A240 - 271

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