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- PDB-3gpx: Sequence-matched MutM Interrogation Complex 4 (IC4) -

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Basic information

Entry
Database: PDB / ID: 3gpx
TitleSequence-matched MutM Interrogation Complex 4 (IC4)
Components
  • DNA (5'-D(*A*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*GP*AP*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: 1.78 Å
AuthorsSpong, M.C. / Qi, 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*TP*CP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*GP*AP*GP*TP*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7334
Polymers38,6683
Non-polymers651
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-23 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.188, 93.541, 104.650
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: 28869.523 Da / Num. of mol.: 1 / Mutation: Q166C, 220-235 deletion
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(*A*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*GP*AP*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 4850.141 Da / Num. of mol.: 1 / Source method: obtained synthetically
#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.: 256 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
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: NSLS / Beamline: X25
DetectorType: ADSC / Detector: CCD / Date: Jul 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 43267 / % possible obs: 99.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Χ2: 1.062 / Net I/σ(I): 26.142
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.78-1.845.40.48542681.003199.9
1.84-1.925.50.32343101.0731100
1.92-25.60.20642801.0421100
2-2.115.60.14643031.0881100
2.11-2.245.70.10143261.0921100
2.24-2.425.70.07743291.0621100
2.42-2.665.60.0643521.0631100
2.66-3.045.60.0543581.0591100
3.04-3.835.50.04344181.044199.9
3.83-5050.03243231.093193.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementResolution: 1.78→41.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2091 5 %RANDOM
Rwork0.189 ---
obs0.19 41809 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.38 Å2 / Biso mean: 30.607 Å2 / Biso min: 10.57 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 489 1 256 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222571
X-RAY DIFFRACTIONr_angle_refined_deg1.3742.223583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3445254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.35321.14987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22315342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9271526
LS refinement shellResolution: 1.78→1.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 108 -
Rwork0.216 2597 -
all-2705 -
obs--88.92 %
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)
10.8026-1.0979-0.77073.24012.3262.9749-0.0293-0.01730.1873-0.02730.0282-0.091-0.14640.18120.0011-0.0354-0.0365-0.0112-0.0308-0.03420.029823.1956-6.4768.5296
20.91640.4992-0.05771.00370.33170.4278-0.0054-0.1194-0.14880.0427-0.09350.03630.1021-0.03180.0989-0.0224-0.00490.01010.0089-0.0047-0.002613.7366-24.27219.5174
31.008-0.1473-0.21280.98140.85910.8981-0.0152-0.02930.1119-0.02-0.03310.0593-0.0545-0.03070.0483-0.00550.0168-0.0035-0.0183-0.0346-0.005215.237-10.82666.7723
40.845-0.2355-0.7931.0429-0.29851.02030.0258-0.14560.03220.09540.0905-0.05420.01190.0884-0.1163-0.02360.01530.00580.0521-0.0295-0.030226.0904-19.40712.7616
50.72840.70510.74471.46021.20441.06190.0301-0.11050.1672-0.046-0.21420.09970.0635-0.09810.1841-0.03480.01240.00780.0383-0.0554-0.00816.6689-12.47438.4674
62.5012-0.00170.30671.11741.26121.4616-0.07080.2127-0.0204-0.4135-0.29160.0478-0.3049-0.23070.36240.03360.1082-0.0887-0.0447-0.1025-0.02764.33638.079414.0641
71.3273-0.07150.22550.80531.38792.48410.123-0.0109-0.05010.049-0.25290.05830.0809-0.1790.1299-0.02030.0159-0.0224-0.0211-0.1084-0.00825.20487.881825.7242
810.0127-4.5754-0.98225.39242.11490.93710.19630.14640.2242-0.4208-0.1606-0.2287-0.3850.0953-0.03570.0450.01820.0136-0.0471-0.0353-0.029713.863912.388919.5446
91.83321.18591.16192.70932.0881.94390.11770.03230.0320.2865-0.0468-0.01410.27890.0887-0.07090.0256-0.0033-0.014-0.0331-0.0614-0.04214.89267.8736.2364
102.7399-0.5499-0.27832.437-0.15320.2545-0.1385-0.2603-0.0880.23720.16180.48950.0263-0.0072-0.02330.00450.00640.050.013-0.04210.00214.254-12.489228.0329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 47
3X-RAY DIFFRACTION3A48 - 78
4X-RAY DIFFRACTION4A79 - 112
5X-RAY DIFFRACTION5A113 - 133
6X-RAY DIFFRACTION6A134 - 152
7X-RAY DIFFRACTION7A153 - 200
8X-RAY DIFFRACTION8A201 - 216
9X-RAY DIFFRACTION9A238 - 274
10X-RAY DIFFRACTION10B2 - 14
11X-RAY DIFFRACTION10C5 - 15

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