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- PDB-3sau: MUTM Interrogation complex 6 -

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Basic information

Entry
Database: PDB / ID: 3sau
TitleMUTM Interrogation complex 6
Components
  • 5'-D(*A*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3'
  • 5'-D(*TP*GP*CP*GP*T*CP*CP*TP*GP*GP*(TX2) P*CP*TP*AP*CP*C)-3'
  • DNA GLYCOSYLASE
KeywordsHYDROLASE/DNA / DNA GLYCOSYLASE / DNA REPAIR / DAMAGE SEARCH / TRANSLOCATION / DISULFIDE CROSSLINKING / DNA DAMAGE / DNA-BINDING / GLYCOSIDASE / HYDROLASE / LYASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / ZINC-FINGER / 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: 1.65 Å
AuthorsSpong, M.C. / Qi, Y. / Verdine, G.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Strandwise translocation of a DNA glycosylase on undamaged DNA.
Authors: Qi, Y. / Nam, K. / Spong, M.C. / Banerjee, A. / Sung, R.J. / Zhang, M. / Karplus, M. / Verdine, G.L.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_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: DNA GLYCOSYLASE
B: 5'-D(*A*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3'
C: 5'-D(*TP*GP*CP*GP*T*CP*CP*TP*GP*GP*(TX2) P*CP*TP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5064
Polymers40,4413
Non-polymers651
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-21 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.423, 93.436, 104.920
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 DNA GLYCOSYLASE


Mass: 30583.330 Da / Num. of mol.: 1 / Mutation: Q166C
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 5'-D(*A*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 5'-D(*TP*GP*CP*GP*T*CP*CP*TP*GP*GP*(TX2) P*CP*TP*AP*CP*C)-3'


Mass: 4900.261 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.: 257 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 291 K / pH: 7
Details: PEG 8K, SODIUM CACODYLATE, GLYCEROL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 52738 / % possible obs: 96.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.493 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GPX

3gpx


Resolution: 1.65→25.25 Å / SU ML: 1.1 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 2529 5.04 %
Rwork0.188 --
obs0.189 50212 92.1 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.19 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.099 Å20 Å2-0 Å2
2--1.623 Å20 Å2
3----1.524 Å2
Refinement stepCycle: LAST / Resolution: 1.65→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 450 1 257 2666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062504
X-RAY DIFFRACTIONf_angle_d1.0863481
X-RAY DIFFRACTIONf_dihedral_angle_d19.058964
X-RAY DIFFRACTIONf_chiral_restr0.068389
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.651-1.6820.271290.2352134X-RAY DIFFRACTION75
1.682-1.7170.2271440.2252337X-RAY DIFFRACTION84
1.717-1.7540.2471290.2042378X-RAY DIFFRACTION84
1.754-1.7950.2251180.1992518X-RAY DIFFRACTION89
1.795-1.8390.2371490.1962515X-RAY DIFFRACTION89
1.839-1.8890.2061320.1862576X-RAY DIFFRACTION90
1.889-1.9450.21350.1642690X-RAY DIFFRACTION94
1.945-2.0080.1781510.1712673X-RAY DIFFRACTION94
2.008-2.0790.1921300.1692772X-RAY DIFFRACTION96
2.079-2.1620.1861470.1692757X-RAY DIFFRACTION97
2.162-2.2610.171360.1662814X-RAY DIFFRACTION98
2.261-2.380.1951500.1752801X-RAY DIFFRACTION98
2.38-2.5290.2281590.1812805X-RAY DIFFRACTION98
2.529-2.7240.2161430.1932832X-RAY DIFFRACTION98
2.724-2.9980.2161630.1912850X-RAY DIFFRACTION99
2.998-3.4310.1841510.192884X-RAY DIFFRACTION99
3.431-4.3190.1921330.1652803X-RAY DIFFRACTION95
4.319-25.2570.2561300.2072544X-RAY DIFFRACTION82
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)
1-0.0885-0.09410.2991.2494-1.13521.16-0.0075-0.0534-0.0346-0.0242-0.0911-0.07470.06410.050.08310.13510.01220.01790.16760.06030.1598-13.986351.053817.1255
22.3579-1.67562.56723.959-0.30041.1486-0.5023-0.74460.67230.81490.458-1.0779-0.1347-0.00750.04380.44980.0354-0.05380.6915-0.03470.5632-3.442658.893626.7496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B OR CHAIN C

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