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- PDB-4pdi: Crystal structure of a complex between an inhibited LlFpg and a N... -

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Basic information

Entry
Database: PDB / ID: 4pdi
TitleCrystal structure of a complex between an inhibited LlFpg and a N7-Benzyl-Fapy-dG containing DNA
Components
  • DNA (5'-D(*CP*TP*CP*TP*TP*TP*(SOS)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 / DNA GLYCOSYLASE / 2TX INHIBITOR / Hydrolase-DNA complex
Function / homology
Function and homology information


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 / 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-sulfanyl-1,9-dihydro-6H-purin-6-one / 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: 2.1 Å
AuthorsCoste, F. / Castaing, B.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Authors: Biela, A. / Coste, F. / Culard, F. / Guerin, M. / Goffinont, S. / Gasteiger, K. / Ciesla, J. / Winczura, A. / Kazimierczuk, Z. / Gasparutto, D. / Carell, T. / Tudek, B. / Castaing, B.
History
DepositionApr 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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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*(SOS)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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9504
Polymers39,7823
Non-polymers1681
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-22 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.535, 91.535, 140.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#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 / Production host: Escherichia coli (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase
#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*TP*TP*(SOS)P*TP*TP*TP*CP*TP*CP*G)-3')


Mass: 4309.889 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)
#4: Chemical ChemComp-2ON / 2-sulfanyl-1,9-dihydro-6H-purin-6-one


Mass: 168.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.86 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.1→47.67 Å / Num. obs: 66600 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 17
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C58

3c58


Resolution: 2.1→47.67 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.79 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 3359 5.04 %Random selection
Rwork0.16 ---
obs0.1616 66600 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 576 11 289 2996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082836
X-RAY DIFFRACTIONf_angle_d1.0753931
X-RAY DIFFRACTIONf_dihedral_angle_d18.9691109
X-RAY DIFFRACTIONf_chiral_restr0.044441
X-RAY DIFFRACTIONf_plane_restr0.005403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13160.30651200.25822639X-RAY DIFFRACTION99
2.1316-2.16350.29811330.24332619X-RAY DIFFRACTION100
2.1635-2.19730.27751810.21652603X-RAY DIFFRACTION100
2.1973-2.23330.26961720.20922624X-RAY DIFFRACTION100
2.2333-2.27180.24931130.19252656X-RAY DIFFRACTION100
2.2718-2.31310.23151250.19362616X-RAY DIFFRACTION100
2.3131-2.35760.22871500.18872657X-RAY DIFFRACTION100
2.3576-2.40570.22771330.17542649X-RAY DIFFRACTION100
2.4057-2.4580.22341570.17892606X-RAY DIFFRACTION100
2.458-2.51520.21161180.18682665X-RAY DIFFRACTION100
2.5152-2.57810.26351390.18142615X-RAY DIFFRACTION100
2.5781-2.64780.23871310.18912653X-RAY DIFFRACTION100
2.6478-2.72570.22391140.19442669X-RAY DIFFRACTION100
2.7257-2.81370.22731370.19822642X-RAY DIFFRACTION100
2.8137-2.91420.23541900.1882576X-RAY DIFFRACTION100
2.9142-3.03090.25221320.19652653X-RAY DIFFRACTION100
3.0309-3.16880.22611390.17742644X-RAY DIFFRACTION100
3.1688-3.33580.1741560.16762597X-RAY DIFFRACTION100
3.3358-3.54480.14341380.13652669X-RAY DIFFRACTION100
3.5448-3.81830.16921450.13652639X-RAY DIFFRACTION100
3.8183-4.20240.13961500.12342621X-RAY DIFFRACTION100
4.2024-4.810.13451360.10942634X-RAY DIFFRACTION100
4.81-6.05810.15251230.12392643X-RAY DIFFRACTION100
6.0581-47.68680.15191270.14752652X-RAY DIFFRACTION100
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)
11.05691.176-0.62752.0542-0.46131.7845-0.0167-0.1218-0.2606-0.1454-0.1005-0.52780.03080.12580.12280.24460.01880.02860.22440.01670.3732-3.28397.777611.7015
21.76330.4193-0.79711.6545-0.48231.39340.1712-0.15010.14260.0982-0.2314-0.228-0.25270.08950.06350.2621-0.0178-0.00420.1869-0.01290.2739-5.000216.266616.1207
33.5961-0.3005-1.19571.2445-0.24851.6697-0.0020.2436-0.0156-0.1834-0.0314-0.21550.0966-0.02550.04090.24210.03150.03680.2139-0.02010.2775-7.20467.97383.7682
40.91690.8219-0.64581.8605-1.2992.0680.1881-0.2114-0.01220.4343-0.2091-0.1707-0.29250.12670.01390.3272-0.0369-0.02610.2914-0.01480.2904-11.04089.902126.9183
51.55940.39890.3631.82920.17093.36430.0978-0.229-0.02060.2093-0.19780.13340.2562-0.42940.10820.3152-0.0860.01290.3122-0.01990.323-23.1294-5.993830.368
64.03031.0523-2.67831.8009-1.26914.4908-0.1873-0.287-0.32710.1956-0.064-0.32510.56960.17150.23620.4018-0.036-0.02080.25550.03070.3952-12.6915-10.559730.5755
76.87193.6451-1.30953.39160.30110.9921-0.44320.4641-0.5281-0.70940.19-0.59020.4044-0.00650.26290.4732-0.01220.06070.3073-0.02130.4363-9.9731-11.075113.0703
83.55551.0142-2.48748.82362.75814.485-0.26630.0164-0.8913-0.0089-0.19190.02880.7853-0.40950.39850.481-0.14970.06550.3969-0.04260.4232-25.3874-20.049816.4883
91.43710.7217-1.00465.0786-2.48753.6373-0.00770.102-0.26940.4303-0.18560.2560.3809-0.35460.21070.4112-0.13180.04930.3479-0.03720.3915-27.6264-14.371722.2952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 141 )
5X-RAY DIFFRACTION5chain 'A' and (resid 142 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 213 )
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 239 )
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 257 )
9X-RAY DIFFRACTION9chain 'A' and (resid 258 through 271 )

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