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- PDB-3u6m: Structural effects of sequence context on lesion recognition by MutM -

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Basic information

Entry
Database: PDB / ID: 3u6m
TitleStructural effects of sequence context on lesion recognition by MutM
Components
  • DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*TP*(8OG)P*GP*TP*(CX2)P*TP*AP*CP*C)-3')
  • Formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / DNA repair / sequence context / lesion recognition / disulfide crosslinking / HYDROLASE-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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM.
Authors: Sung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase
B: DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*TP*(8OG)P*GP*TP*(CX2)P*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5194
Polymers40,4543
Non-polymers651
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-11 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.188, 93.541, 104.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Formamidopyrimidine-DNA glycosylase


Mass: 30580.330 Da / Num. of mol.: 1 / Mutation: E3Q, Q166C,V222P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P84131, DNA-formamidopyrimidine glycosylase
#2: DNA chain DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3')


Mass: 4957.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*TP*(8OG)P*GP*TP*(CX2)P*TP*AP*CP*C)-3')


Mass: 4916.261 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.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8K, sodium cacodylate, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→32.685 Å / Num. obs: 25999
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.685 Å / SU ML: 0.26 / σ(F): 0.21 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1219 4.82 %
Rwork0.1883 --
obs0.19 25296 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.943 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3747 Å2-0 Å2-0 Å2
2---3.8965 Å20 Å2
3----1.4782 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 357 1 144 2492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052451
X-RAY DIFFRACTIONf_angle_d0.9533383
X-RAY DIFFRACTIONf_dihedral_angle_d17.219959
X-RAY DIFFRACTIONf_chiral_restr0.059374
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.25191410.20162411X-RAY DIFFRACTION88
2.1841-2.28340.21591130.18782475X-RAY DIFFRACTION89
2.2834-2.40380.25511210.17762574X-RAY DIFFRACTION93
2.4038-2.55440.2491240.18922604X-RAY DIFFRACTION93
2.5544-2.75150.22261520.18532664X-RAY DIFFRACTION96
2.7515-3.02820.22651330.19182739X-RAY DIFFRACTION97
3.0282-3.4660.22961430.19932795X-RAY DIFFRACTION99
3.466-4.36510.18891440.17052831X-RAY DIFFRACTION100
4.3651-32.68850.21211480.18222984X-RAY DIFFRACTION99
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)
1-0.22380.12590.05631.19821.12941.103-0.0134-0.06250.01940.0062-0.14650.1095-0.0176-0.0860.14170.03820.0124-0.00540.1445-0.05270.079113.7583-4.106517.2455
24.626-4.626-1.96186.49621.41710.9541-0.36350.0834-0.53750.7446-0.02990.83170.08840.00370.37040.3278-0.14230.06470.3233-0.04550.34614.2966-11.748726.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B or chain C

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