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- PDB-3c58: Crystal structure of a complex between the wild-type lactococcus ... -

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Basic information

Entry
Database: PDB / ID: 3c58
TitleCrystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA
Components
  • DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3')
  • DNA (5'-D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3')
  • DNA glycosylase
KeywordsHYDROLASE/DNA / Protein-DNA complex / Glycosylase / Benzyl-Fapy / DNA repair / Hydrolase-DNA complex / DNA damage / DNA-binding / Glycosidase / Lyase / Metal-binding / Multifunctional enzyme / Zinc-finger
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
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCoste, F. / Castaing, B. / Carell, T.
CitationJournal: Chem.Biol. / Year: 2008
Title: Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode
Authors: Coste, F. / Ober, M. / Le Bihan, Y.V. / Izquierdo, M.A. / Hervouet, N. / Mueller, H. / Carell, T. / Castaing, B.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3')
B: DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3')
A: DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9395
Polymers39,7823
Non-polymers1582
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-22.5 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.356, 91.356, 140.943
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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DNA chain , 2 types, 2 molecules CB

#1: DNA chain DNA (5'-D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3')


Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#2: DNA chain DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3')


Mass: 4309.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA

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Protein , 1 types, 1 molecules A

#3: Protein 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 (lactic acid bacteria)
Gene: MUTM, FPG / Variant: Subsp. Cremoris / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A2RI84, UniProt: P42371*PLUS, DNA-(apurinic or apyrimidinic site) lyase

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Non-polymers , 3 types, 337 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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.: 335 / 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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, Sodium citrate, PH7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2Sodium citrate11
3HOH11
4HEPES12
5Sodium citrate12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935 / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2006
RadiationMonochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.9→47.62 Å / Num. all: 47718 / Num. obs: 47718 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 23.67 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 17
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.451 / % possible all: 100

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XC8

1xc8


Resolution: 1.9→45.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2411 5.1 %RANDOM
Rwork0.172 ---
all0.173 45259 --
obs0.173 45259 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.9→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 576 7 335 3044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222832
X-RAY DIFFRACTIONr_angle_refined_deg1.7452.2363924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77524.57494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29115423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9971512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021889
X-RAY DIFFRACTIONr_nbd_refined0.2170.21250
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.211
X-RAY DIFFRACTIONr_mcbond_it1.1141.51408
X-RAY DIFFRACTIONr_mcangle_it1.62122168
X-RAY DIFFRACTIONr_scbond_it2.60231794
X-RAY DIFFRACTIONr_scangle_it3.7694.51756
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 152 -
Rwork0.238 3304 -
obs--100 %

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