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- PDB-6rp7: The crystal structure of a complex between the LlFpg protein, a T... -

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Basic information

Entry
Database: PDB / ID: 6rp7
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
6,7-dimethyl-2-sulfanylidene-1~{H}-pteridin-4-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 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 14, 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)39,8275
Polymers39,5273
Non-polymers3002
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-21 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.669, 91.669, 141.043
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: 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, 179 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KD8 / 6,7-dimethyl-2-sulfanylidene-1~{H}-pteridin-4-one


Mass: 208.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N4OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.8 Å3/Da / Density % sol: 67.63 %
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→47.72 Å / Num. obs: 41266 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Num. unique obs: 5925 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PM5

1pm5


Resolution: 2→45.834 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 3827 4.94 %
Rwork0.1658 73639 -
obs0.1668 77466 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.43 Å2 / Biso mean: 52.5569 Å2 / Biso min: 29.43 Å2
Refinement stepCycle: final / Resolution: 2→45.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 557 20 177 2859
Biso mean--51.76 53.72 -
Num. residues----295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02530.28631490.300727362885100
2.0253-2.0520.30721580.288327252883100
2.052-2.08010.29541370.274827202857100
2.0801-2.10980.27351280.263227232851100
2.1098-2.14130.24211540.240327362890100
2.1413-2.17470.27461440.231427402884100
2.1747-2.21040.21561290.215527232852100
2.2104-2.24850.21481570.198827372894100
2.2485-2.28940.23381490.194927022851100
2.2894-2.33340.22451710.195626982869100
2.3334-2.38110.18831570.178126972854100
2.3811-2.43280.20981470.165327612908100
2.4328-2.48940.17661570.176627262883100
2.4894-2.55170.20461250.181327322857100
2.5517-2.62070.25751350.198227542889100
2.6207-2.69780.2431630.212927162879100
2.6978-2.78480.22351170.203927372854100
2.7848-2.88430.28881310.201727362867100
2.8843-2.99980.23261630.202327142877100
2.9998-3.13630.2151190.188627312850100
3.1363-3.30160.16461400.17427582898100
3.3016-3.50840.20111330.149427232856100
3.5084-3.77920.18581140.143427352849100
3.7792-4.15930.13521640.13592697286199
4.1593-4.76060.12931490.116527202869100
4.7606-5.99570.15681170.13082733285099
5.9957-45.84650.13741200.15512729284999
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)
14.06730.25791.45993.271-0.68692.9279-0.1934-0.23650.2702-0.31640.15840.6984-0.2479-0.89540.06310.47290.0212-0.04770.497-0.02410.4752-30.79043.347211.479
28.15154.4227-5.90198.1927-2.58984.4302-0.43420.29690.5194-0.09290.24280.06421.1135-0.98750.31890.48160.1416-0.0130.8601-0.09840.5251-33.63076.020619.3993
33.6855.48040.92959.69822.88832.5227-0.00550.4896-1.0171-1.11660.12820.08540.7055-0.6145-0.13140.708-0.0684-0.15880.5553-0.10150.5972-25.1976-1.8942-0.2161
48.61131.3023-2.03382.80650.14563.69790.1271-0.209-0.63820.006-0.14-0.36850.25490.14320.03620.38180.04130.00350.32220.07760.5199-3.33090.511416.5139
53.21710.4624-0.76162.6615-0.84622.51240.2132-0.13650.28760.0239-0.201-0.2887-0.35630.22430.00250.4343-0.01780.0240.2741-0.02170.3651-4.398415.840413.7876
65.5850.2691-4.76621.7943-1.50348.5458-0.07640.7357-0.1662-0.27180.0845-0.08860.3601-0.3568-0.02360.40640.0201-0.00080.3244-0.05330.3693-7.54285.55462.7691
71.37960.479-0.47251.3709-0.42912.2160.153-0.1326-0.05660.1165-0.1273-0.167-0.20260.0932-0.02430.36770.0094-0.00020.2992-0.02160.3702-9.51449.90617.6741
82.62520.5138-0.80923.55551.19478.03630.0942-0.2462-0.15670.2318-0.23030.12040.389-0.58350.14890.3336-0.0914-0.02510.34720.02420.3873-23.0465-6.094330.546
95.35744.0153-4.85185.0297-3.58244.6087-0.1247-0.9566-0.50440.2982-0.3436-0.58030.48871.09390.40810.4824-0.0074-0.06960.35940.09570.4999-12.4918-10.314330.7261
106.50996.22371.31748.50861.5240.2813-0.51950.4211-1.143-0.74710.3358-1.09160.65010.15050.2210.73440.02070.09240.462-0.05920.7082-9.6279-10.942513.2261
116.9126-4.3753-5.33512.91613.53364.2725-0.5956-0.4916-1.6754-0.51840.20110.95510.9971-0.15270.30190.6534-0.13270.0510.4698-0.00380.6801-25.4566-19.977916.868
124.59381.6435-1.515.2343-4.4534.03360.14150.05-0.6290.644-0.48520.0070.07960.07870.27090.5824-0.15290.01240.4506-0.05390.545-27.4726-14.56922.5884
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 16 )A1 - 16
5X-RAY DIFFRACTION5chain 'A' and (resid 17 through 72 )A17 - 72
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 91 )A73 - 91
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 141 )A92 - 141
8X-RAY DIFFRACTION8chain 'A' and (resid 142 through 193 )A142 - 193
9X-RAY DIFFRACTION9chain 'A' and (resid 194 through 213 )A194 - 213
10X-RAY DIFFRACTION10chain 'A' and (resid 214 through 239 )A214 - 239
11X-RAY DIFFRACTION11chain 'A' and (resid 240 through 257 )A240 - 257
12X-RAY DIFFRACTION12chain 'A' and (resid 258 through 271 )A258 - 271

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