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- PDB-3u6p: MutM set 1 GpG -

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Basic information

Entry
Database: PDB / ID: 3u6p
TitleMutM set 1 GpG
Components
  • DNA (5'-D(*A*GP*GP*TP*AP*GP*AP*TP*CP*CP*CP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*CP*GP*GP*GP*AP*(08Q)P*CP*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 / double-stranded DNA binding / 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: 1.6 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 20, 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(*A*GP*GP*TP*AP*GP*AP*TP*CP*CP*CP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*TP*CP*GP*GP*GP*AP*(08Q)P*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5034
Polymers40,4383
Non-polymers651
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area14630 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(*A*GP*GP*TP*AP*GP*AP*TP*CP*CP*CP*GP*AP*CP*GP*C)-3')


Mass: 4908.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*CP*GP*GP*GP*AP*(08Q)P*CP*TP*AP*CP*C)-3')


Mass: 4949.299 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.: 331 / 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: 55.02 %
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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→32.685 Å / Num. obs: 58218
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.4

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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: 1.6→29.882 Å / SU ML: 0.17 / σ(F): 0.12 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 2699 4.85 %
Rwork0.1926 --
obs0.1933 55594 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.778 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4258 Å2-0 Å2-0 Å2
2---0.0364 Å20 Å2
3----1.3894 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 472 1 331 2788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052661
X-RAY DIFFRACTIONf_angle_d1.2683712
X-RAY DIFFRACTIONf_dihedral_angle_d17.8421066
X-RAY DIFFRACTIONf_chiral_restr0.215409
X-RAY DIFFRACTIONf_plane_restr0.003393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62910.12740.2332490X-RAY DIFFRACTION81
1.6291-1.66040.25081390.2172579X-RAY DIFFRACTION88
1.6604-1.69430.24781190.20052651X-RAY DIFFRACTION90
1.6943-1.73120.181710.19752698X-RAY DIFFRACTION92
1.7312-1.77140.23181470.1972674X-RAY DIFFRACTION92
1.7714-1.81570.21771460.19052735X-RAY DIFFRACTION93
1.8157-1.86480.20961520.19112759X-RAY DIFFRACTION94
1.8648-1.91970.21191470.18452771X-RAY DIFFRACTION94
1.9197-1.98160.20981660.18132800X-RAY DIFFRACTION96
1.9816-2.05240.18531280.1782871X-RAY DIFFRACTION97
2.0524-2.13460.16571450.18262867X-RAY DIFFRACTION97
2.1346-2.23170.19591450.17892866X-RAY DIFFRACTION97
2.2317-2.34930.19531630.18672845X-RAY DIFFRACTION97
2.3493-2.49640.21231600.19362858X-RAY DIFFRACTION96
2.4964-2.68910.22671560.2072858X-RAY DIFFRACTION96
2.6891-2.95950.23511440.20222889X-RAY DIFFRACTION96
2.9595-3.38720.18641470.19722883X-RAY DIFFRACTION96
3.3872-4.26550.18311550.16452904X-RAY DIFFRACTION95
4.2655-29.88740.21081650.20022897X-RAY DIFFRACTION91
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)
1-0.1042-0.0015-0.06861.06150.92010.9068-0.0001-0.03930.0327-0.0387-0.12110.1137-0.0567-0.07020.10280.09090.0085-0.00630.1448-0.04830.132813.8364-4.15816.9687
21.856-2.0344-2.15934.70741.4012.8656-0.4544-0.3007-0.43540.45710.341.00360.1444-0.25460.12560.18530.01470.09870.3758-0.03430.3954.8196-11.696327.5781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B or chain C

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