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- PDB-3jr4: MutM interrogating an extrahelical G -

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Basic information

Entry
Database: PDB / ID: 3jr4
TitleMutM interrogating an extrahelical G
Components
  • DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*G*CP*GP*TP*CP*CP*AP*(GX1)P*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 / Zinc-finger / Lyase-DNA COMPLEX
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion 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 / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsQi, Y. / Spong, M.C. / Verdine, G.L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
Authors: Qi, Y. / Spong, M.C. / Nam, K. / Karplus, M. / Verdine, G.L.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 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.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_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*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*G*CP*GP*TP*CP*CP*AP*(GX1)P*GP*TP*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5194
Polymers40,4543
Non-polymers651
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.343, 95.377, 102.482
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: 30596.373 Da / Num. of mol.: 1 / Fragment: MutM / Mutation: N174C
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*CP*CP*TP*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*G*CP*GP*TP*CP*CP*AP*(GX1)P*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 4909.275 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 / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
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: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14207 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.103 / Χ2: 1.004 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.697.20.54813881.015100
2.69-2.87.30.42113930.98100
2.8-2.937.20.31813920.983100
2.93-3.087.20.22913861.013100
3.08-3.287.20.15214011.009100
3.28-3.537.10.10614100.983100
3.53-3.887.10.09314080.972100
3.88-4.4570.07714321.035100
4.45-5.66.80.05614541.064100
5.6-506.60.04415430.98399.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R2Y

1r2y


Resolution: 2.601→45.139 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 682 5.03 %
Rwork0.19 --
obs0.193 13557 95.06 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.821 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 193.49 Å2 / Biso mean: 45.801 Å2 / Biso min: 11.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.498 Å20 Å2-0 Å2
2--0.345 Å20 Å2
3----1.843 Å2
Refinement stepCycle: LAST / Resolution: 2.601→45.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 451 1 64 2550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052584
X-RAY DIFFRACTIONf_angle_d0.9513588
X-RAY DIFFRACTIONf_chiral_restr0.055400
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d19.194987
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.601-2.8020.3251180.2272292241086
2.802-3.0830.2941350.2122472260793
3.083-3.5290.2431480.1912612276098
3.529-4.4460.2021490.1582665281499
4.446-45.1460.2031320.1822834296699
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)
1-0.1151-0.10320.10161.3504-1.09821.3705-0.0099-0.0871-0.0205-0.0802-0.0553-0.10430.09190.05510.06390.13360.0098-0.00520.20560.02260.1769-13.975552.194417.3265
22.0105-0.2333.12693.95960.641-0.1964-0.3106-0.7266-0.0061.32730.5079-0.6160.3458-0.3206-0.26190.8150.14460.05240.96790.03140.599-14.165861.360734.3157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 274
2X-RAY DIFFRACTION2chain B or chain CB5 - 15
3X-RAY DIFFRACTION2chain B or chain CC3 - 13

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