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- PDB-3gpy: Sequence-matched MutM Lesion Recognition Complex 3 (LRC3) -

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Basic information

Entry
Database: PDB / ID: 3gpy
TitleSequence-matched MutM Lesion Recognition Complex 3 (LRC3)
Components
  • DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*T*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*CP*C)-3')
  • DNA glycosylase
KeywordsLyase/DNA / DNA glycosylase / DNA repair / damage search / base extrusion / disulfide crosslinking / DNA damage / DNA-binding / Glycosidase / Hydrolase / Lyase / Metal-binding / Multifunctional enzyme / Zinc-finger / Lyase-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
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsQi, Y. / Verdine, G.L.
CitationJournal: Nature / Year: 2009
Title: Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.
Authors: Qi, Y. / Spong, M.C. / Nam, K. / Banerjee, A. / Jiralerspong, S. / Karplus, M. / Verdine, G.L.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA glycosylase
B: DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*T*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4624
Polymers40,3973
Non-polymers651
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-20 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.904, 95.207, 102.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA glycosylase


Mass: 30582.346 Da / Num. of mol.: 1 / Mutation: Q166C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: MutM / Plasmid: pET24B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS
References: UniProt: P84131, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA (5'-D(*T*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*CP*C)-3')


Mass: 4866.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8K, sodium cacodylate, glycerol, pH 7.0, vapor diffusion, hanging drop, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 8K11
2sodium cacodylate11
3glycerol11
4PEG 8K12
5sodium cacodylate12
6glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC / Detector: CCD / Date: Aug 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 37987 / % possible obs: 99.8 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.13 / Χ2: 1.008 / Net I/σ(I): 13.179
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.927.90.63137250.9721100
1.92-1.998.30.51337441.0341100
1.99-2.088.60.3837451.0381100
2.08-2.198.60.28837541.021100
2.19-2.338.60.21837821.0331100
2.33-2.518.60.17637731.0051100
2.51-2.768.60.14137951.0021100
2.76-3.168.50.11838191199.9
3.16-3.998.40.10438531.001199.7
3.99-508.10.07939970.971198.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementStarting model: pdb entry 1R2Y, protein part only

1r2y


Resolution: 1.85→47.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1820 5 %RANDOM
Rwork0.164 ---
obs0.165 36463 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.04 Å2 / Biso mean: 25.714 Å2 / Biso min: 9.74 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 631 1 297 3056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212902
X-RAY DIFFRACTIONr_angle_refined_deg1.3912.2464063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.81921.44397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73715369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031527
LS refinement shellResolution: 1.85→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 123 -
Rwork0.176 2280 -
all-2403 -
obs--89.07 %
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)
10.2301-0.12380.12680.3074-0.26150.731-0.0074-0.0314-0.0083-0.0180.0045-0.0066-0.0063-0.0110.00290.0170.00490.00030.01430.0052-0.0446-17.69763.3759.641
27.3195-3.1873-1.442212.186-6.488610.2720.0980.0336-0.16120.013-0.6101-0.6473-0.14510.50350.5121-0.04620.02570.02330.05460.0849-0.0622-1.6257.4077.092
30.2238-0.0654-0.13060.4126-0.35831.21890.0226-0.03080.0118-0.1206-0.1664-0.07260.13560.10150.14380.00030.0470.04420.02260.0695-0.0124-4.36540.07422.436
412.7056-4.80663.94393.7993-2.67061.9811-0.00550.1162-0.3202-0.4617-0.04320.01530.3816-0.02870.04870.10820.020.0552-0.04670.0123-0.069-12.54435.37418.873
50.1741-0.72280.58323.2787-1.89122.96240.094-0.1162-0.1131-0.07430.21110.14390.0643-0.3981-0.305-0.0365-0.0162-0.00650.05020.0469-0.0239-25.46746.77521.356
60.75460.3546-0.6492.4361-1.12050.85120.0758-0.0291-0.00310.1082-0.1115-0.0302-0.0450.02390.03580.0224-0.0197-0.008-0.00210.0325-0.0361-14.99339.84736.073
71.6372-1.21761.35241.5379-1.32911.2824-0.2278-0.01370.03210.40770.1274-0.1685-0.2549-0.07670.10040.07510.0117-0.01670.0122-0.0048-0.0613-8.1559.14433.839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 123
2X-RAY DIFFRACTION2A124 - 133
3X-RAY DIFFRACTION3A134 - 200
4X-RAY DIFFRACTION4A201 - 215
5X-RAY DIFFRACTION5A216 - 240
6X-RAY DIFFRACTION6A241 - 274
7X-RAY DIFFRACTION7B1 - 16
8X-RAY DIFFRACTION7C1 - 15

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