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

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Basic information

Entry
Database: PDB / ID: 6rnr
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


oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-formamidopyrimidine glycosylase / 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. / 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
2-(trifluoromethyl)-9~{H}-purine-6-thiol / 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: 2.003 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _software.name

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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)39,9545
Polymers39,6423
Non-polymers3122
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-24 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.813, 91.813, 141.617
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 / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase MutM / AP lyase MutM


Mass: 31231.303 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, 114 molecules

#4: Chemical ChemComp-KBN / 2-(trifluoromethyl)-9~{H}-purine-6-thiol


Mass: 220.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3F3N4S / 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.: 112 / 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: 3.84 Å3/Da / Density % sol: 67.93 %
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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→47.21 Å / Num. obs: 41111 / % possible obs: 98.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 41.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.7
Reflection shellResolution: 2→2.04 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2048 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PM5

1pm5


Resolution: 2.003→45.907 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.89
RfactorNum. reflection% reflection
Rfree0.195 2109 5.14 %
Rwork0.1739 --
obs0.175 41035 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.93 Å2 / Biso mean: 50.0701 Å2 / Biso min: 26.62 Å2
Refinement stepCycle: final / Resolution: 2.003→45.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 557 20 112 2806
Biso mean--58.61 45.76 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082821
X-RAY DIFFRACTIONf_angle_d0.9793917
X-RAY DIFFRACTIONf_chiral_restr0.056438
X-RAY DIFFRACTIONf_plane_restr0.005399
X-RAY DIFFRACTIONf_dihedral_angle_d18.1431627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0026-2.04920.24971160.238725942710100
2.0492-2.10050.28371610.2325462707100
2.1005-2.15720.23891430.212125802723100
2.1572-2.22070.22611330.191425782711100
2.2207-2.29240.23621280.18722233236186
2.2924-2.37430.23991440.192125752719100
2.3743-2.46940.23611340.186826022736100
2.4694-2.58180.24581530.199625662719100
2.5818-2.71790.27891460.222826062752100
2.7179-2.88810.29391330.22632605273899
2.8881-3.11110.28691480.225226212769100
3.1111-3.42410.20651290.18682640276999
3.4241-3.91930.16051460.154926442790100
3.9193-4.9370.12091540.12426912845100
4.937-45.91850.16091410.15412845298699
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)
11.47620.5683-0.16272.5313-0.67821.90060.027-0.10520.1679-0.333-0.04280.6905-0.0741-0.82470.01480.45620.0514-0.08190.5132-0.07830.49-30.68753.47911.4591
24.48071.0916-0.72572.5839-0.71153.7977-0.0474-0.0356-0.0259-0.08270.23270.25090.3783-0.839-0.13290.32360.0359-0.07270.5651-0.06840.3544-29.91582.921311.003
33.47620.7635-0.66462.0652-0.77273.40120.1472-0.16220.0628-0.0711-0.2239-0.3734-0.30910.27030.06740.356-0.00590.00990.2501-0.02020.3186-3.922812.13114.4931
43.20450.383-1.52090.3019-0.93113.40870.00640.5474-0.1646-0.2530.0366-0.04070.2495-0.2352-0.0860.41390.04670.00950.3529-0.07650.357-7.51736.16432.2754
51.25740.8004-0.75281.7254-0.80863.07180.1328-0.2086-0.17790.1424-0.1724-0.05370.1223-0.1580.0350.3296-0.0031-0.03030.3063-0.01560.3386-16.33121.671824.3538
63.11451.8556-0.80214.6672-1.07141.9013-0.09740.0402-0.5883-0.2956-0.1384-0.71660.39420.41380.30870.53020.0197-0.0240.2890.01890.5369-11.0923-10.871322.5282
78.48410.3117-4.14552.87273.50196.7179-0.3595-0.0715-1.3922-0.405-0.09050.18110.80960.05240.48850.5679-0.12740.02780.4769-0.05720.5964-25.2861-19.456916.7099
81.6072.3136-2.0565.8497-3.28064.4677-0.07310.1256-0.50950.6391-0.2855-0.30370.4497-0.54480.36770.7073-0.20960.01790.4421-0.0530.5377-27.4981-14.477622.4701
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 28 )E15 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 72 )A1 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 91 )A73 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 193 )A92 - 193
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 239 )A194 - 239
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 257 )A240 - 257
8X-RAY DIFFRACTION8chain 'A' and (resid 258 through 271 )A258 - 271

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