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- PDB-4pdg: Crystal structure of a complex between an inhibited LlFpg and a T... -

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Basic information

Entry
Database: PDB / ID: 4pdg
TitleCrystal structure of a complex between an inhibited LlFpg and a THF containing DNA
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 / DNA GLYCOSYLASE / 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. / 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-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: 2.4 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
Revision 1.2Nov 6, 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7875
Polymers39,5273
Non-polymers2602
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-27 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.550, 90.550, 139.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Production host: Escherichia coli (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase

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DNA chain , 2 types, 2 molecules BC

#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, 60 molecules

#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: 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.: 58 / 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

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.96 %
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: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.4→43.06 Å / Num. obs: 43014 / % possible obs: 99.1 % / Redundancy: 4.8 % / Net I/σ(I): 16.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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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 1PM5

1pm5


Resolution: 2.4→43.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 2208 5.13 %Random selection
Rwork0.1632 ---
obs0.1647 43014 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 557 17 58 2733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122780
X-RAY DIFFRACTIONf_angle_d1.2813856
X-RAY DIFFRACTIONf_dihedral_angle_d19.951088
X-RAY DIFFRACTIONf_chiral_restr0.054434
X-RAY DIFFRACTIONf_plane_restr0.006391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44980.3481400.2862581X-RAY DIFFRACTION99
2.4498-2.50680.31781310.27322576X-RAY DIFFRACTION100
2.5068-2.56950.2751650.2662519X-RAY DIFFRACTION100
2.5695-2.6390.25151580.24512536X-RAY DIFFRACTION99
2.639-2.71660.24421480.2282547X-RAY DIFFRACTION100
2.7166-2.80430.24471410.21212565X-RAY DIFFRACTION100
2.8043-2.90450.20551160.20692607X-RAY DIFFRACTION100
2.9045-3.02070.22911430.1952577X-RAY DIFFRACTION100
3.0207-3.15820.18911400.17222521X-RAY DIFFRACTION100
3.1582-3.32460.19611280.15542601X-RAY DIFFRACTION100
3.3246-3.53280.17521540.12682518X-RAY DIFFRACTION99
3.5328-3.80540.16651160.12952573X-RAY DIFFRACTION99
3.8054-4.18810.16711530.12522525X-RAY DIFFRACTION98
4.1881-4.79350.13351200.1132553X-RAY DIFFRACTION98
4.7935-6.03660.17211160.14632541X-RAY DIFFRACTION98
6.0366-43.06630.18481390.17552466X-RAY DIFFRACTION96
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)
13.5509-0.5206-1.03853.91711.81542.98640.16250.15390.0647-0.1099-0.2740.3268-0.2465-0.41220.1220.31460.04840.00580.28750.010.27343.7369102.546120.6708
26.5415-0.6407-2.83161.5991.34013.52-0.0779-0.746-0.17940.28430.1010.18480.22970.14240.04570.41780.02990.03550.30210.04280.30287.065996.284432.4553
31.5398-0.7115-0.67562.00850.79392.55140.10210.086-0.05-0.2135-0.16030.1798-0.2378-0.2620.04680.30740.0283-0.02870.22140.02950.29399.0123100.202217.4426
47.588-1.74074.98875.5424-2.54823.72760.25850.99770.2708-0.4222-0.3169-0.11250.35480.41330.05470.38160.06290.05270.36040.0190.343523.203387.28880.6531
54.0332-2.0071-1.40284.08030.41314.36960.07040.1981-0.4266-0.3301-0.18910.08230.54660.00030.12180.48240.0218-0.05820.2648-0.02870.365418.208580.92396.6649
68.2198-6.40950.27868.5676-0.57890.0275-0.5839-0.2413-1.14840.82220.26271.15730.6221-0.18460.34320.7742-0.05730.08040.44820.04910.547113.279774.872320.7108
72.66170.1664-0.54679.8229-1.93912.69520.14770.1057-0.1074-0.3649-0.3472-0.38380.54680.29360.22650.49230.106-0.01350.33550.02680.410327.400975.016715.1313
82.86550.07820.24394.3134-1.2965.4963-0.01810.18060.42790.4792-0.0927-0.8363-0.2411.17640.18280.5184-0.0228-0.07620.53490.01050.519630.144793.51723.7699
96.17920.353-6.49078.3293-0.57766.9171-0.74940.41160.5994-0.28380.286-0.76331.86340.89290.85070.58650.01050.13220.8680.2480.709532.20195.705215.4526
103.7921-5.3991.02339.185-3.23282.7721-0.0378-0.7845-1.33211.48990.01880.1955-0.03210.42140.12760.68630.0651-0.2090.57060.11570.70924.714488.840735.3849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 161 )
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 248 )
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 271 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 14 )
9X-RAY DIFFRACTION9chain 'C' and (resid 15 through 22 )
10X-RAY DIFFRACTION10chain 'C' and (resid 23 through 28 )

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