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- PDB-3sat: MUTM Slanted complex 6 with R112A mutation -

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Basic information

Entry
Database: PDB / ID: 3sat
TitleMUTM Slanted complex 6 with R112A mutation
Components
  • 5'-D(*AP*GP*G*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 / LYASE-DNA COMPLEX / 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: 2.15 Å
AuthorsQi, 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(*AP*GP*G*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)40,5125
Polymers40,3553
Non-polymers1582
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-13 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.487, 97.574, 102.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA GLYCOSYLASE


Mass: 30497.213 Da / Num. of mol.: 1 / Mutation: R112A, 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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*AP*GP*G*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
#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

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Non-polymers , 3 types, 157 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
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: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 25355 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.406 / % possible all: 100

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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: 2F5O

2f5o


Resolution: 2.15→26.29 Å / SU ML: 2.02 / σ(F): 0.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1160 4.86 %
Rwork0.187 --
obs0.189 23867 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.47 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 45.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.552 Å20 Å2-0 Å2
2--5.163 Å20 Å2
3----2.611 Å2
Refinement stepCycle: LAST / Resolution: 2.15→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 385 7 155 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052417
X-RAY DIFFRACTIONf_angle_d1.0333351
X-RAY DIFFRACTIONf_dihedral_angle_d19.603920
X-RAY DIFFRACTIONf_chiral_restr0.06377
X-RAY DIFFRACTIONf_plane_restr0.005370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.153-2.2510.2211170.1812360X-RAY DIFFRACTION80
2.251-2.370.2241480.182606X-RAY DIFFRACTION88
2.37-2.5180.2311140.1832831X-RAY DIFFRACTION93
2.518-2.7120.2291340.1932879X-RAY DIFFRACTION96
2.712-2.9850.2381560.1992922X-RAY DIFFRACTION98
2.985-3.4160.2321540.1882973X-RAY DIFFRACTION99
3.416-4.3010.1981680.173003X-RAY DIFFRACTION99
4.301-26.2890.2181690.1813133X-RAY DIFFRACTION98
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)
10.011-0.04470.10391.2441-0.85420.8363-0.021-0.08980.02-0.0772-0.1356-0.09170.05930.02250.09870.06080.01290.02770.030.09470.0379-14.04753.871516.9409
22.6796-1.4852.46253.6779-1.99872.2079-0.3217-0.40470.02951.0611-0.0752-0.317-0.5742-0.5430.3910.5521-0.0441-0.04040.5040.03970.3191-5.688762.421628.5223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B OR CHAIN C

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