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- PDB-3gq5: Sequence-matched MutM Interrogation Complex 5 (IC5) -

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Basic information

Entry
Database: PDB / ID: 3gq5
TitleSequence-matched MutM Interrogation Complex 5 (IC5)
Components
  • DNA (5'-D(*A*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*T*CP*CP*GP*GP*GP*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. / 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
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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(*A*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*T*CP*CP*GP*GP*GP*TP*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6286
Polymers40,3793
Non-polymers2503
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-21 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.240, 94.443, 104.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA glycosylase


Mass: 30579.342 Da / Num. of mol.: 1 / Mutation: Q166C, T224P
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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*A*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)-3')


Mass: 4933.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*T*CP*CP*GP*GP*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 4866.140 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 171 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
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-C / Wavelength: 0.979 Å
DetectorType: ADSC / Detector: CCD / Date: Oct 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35968 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.061 / Χ2: 1.018 / Net I/σ(I): 29.259
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.977.30.5235211.0591100
1.97-2.057.30.32335320.9821100
2.05-2.147.30.22735671.0211100
2.14-2.257.30.1635351.0111100
2.25-2.397.30.11635620.9871100
2.39-2.587.30.09335581.0181100
2.58-2.847.30.07236121.0191100
2.84-3.257.10.06136160.9711100
3.25-4.096.80.05236600.9781100
4.09-506.50.03338051.14199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementResolution: 1.9→45.69 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3476 10 %RANDOM
Rwork0.203 ---
obs0.204 34832 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.78 Å2 / Biso mean: 37.505 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 447 13 168 2587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222524
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.2083508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.77121.14987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2111526
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 230 -
Rwork0.201 2053 -
all-2283 -
obs--90.13 %
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)
11.3071-0.40610.14450.3574-0.41470.74780.0141-0.1382-0.0534-0.0514-0.0287-0.0108-0.0062-0.02110.0146-0.0014-0.0103-0.00870.00050.021-0.0608-18.1862.6969.432
20.57910.30970.13941.6444-1.88172.62160.09130.0250.0015-0.0892-0.3624-0.10710.11620.25710.271-0.00490.10430.08380.0040.1554-0.0199-4.60639.87522.405
30.29940.5503-1.06992.0315-2.32193.94680.2855-0.0194-0.0180.1152-0.1339-0.0054-0.1743-0.1444-0.15160.03370.03810.0627-0.04060.0789-0.0708-14.18438.12731.494
45.9194-2.38690.1652.26161.63663.5839-0.5771-0.63840.23180.66560.7031-0.59430.39050.5297-0.1260.0920.0812-0.09230.09090.0347-0.0931-6.12660.52728.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 132
2X-RAY DIFFRACTION2A133 - 200
3X-RAY DIFFRACTION3A201 - 274
4X-RAY DIFFRACTION4B2 - 13
5X-RAY DIFFRACTION4C6 - 15

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