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- PDB-3sbj: MutM slanted complex 7 -

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Basic information

Entry
Database: PDB / ID: 3sbj
TitleMutM slanted complex 7
Components
  • 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*G)-3'
  • 5'-D(P*CP*CP*TP*GP*GP*TP*(CX)P*TP*AP*CP*C)-3'
  • Formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / DNA repair / damage search / translocation / 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. / 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: 2.1 Å
AuthorsSung, R.J. / Zhang, M. / 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 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_conn_type.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: 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*G)-3'
C: 5'-D(P*CP*CP*TP*GP*GP*TP*(CX)P*TP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4144
Polymers37,3493
Non-polymers651
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-22 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.188, 93.541, 104.650
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 Formamidopyrimidine-DNA glycosylase


Mass: 30581.314 Da / Num. of mol.: 1 / Mutation: Q166C, V222P
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
#2: DNA chain 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*G)-3'


Mass: 3423.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain 5'-D(P*CP*CP*TP*GP*GP*TP*(CX)P*TP*AP*CP*C)-3'


Mass: 3344.282 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.: 153 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
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

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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 315 / 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: 2.078→34.2 Å / Num. obs: 26487 / Biso Wilson estimate: 28.97 Å2
Reflection shellHighest resolution: 2.1 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1318 / Rsym value: 0.491

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.685 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8522 / SU ML: 0.25 / σ(F): 0.18 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 1197 4.83 %
Rwork0.1979 --
obs0.1998 24779 92.98 %
all-25976 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.069 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 485.32 Å2 / Biso mean: 47.0561 Å2 / Biso min: 12.41 Å2
Baniso -1Baniso -2Baniso -3
1-5.5725 Å2-0 Å2-0 Å2
2---0.8346 Å20 Å2
3----4.7379 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 451 1 153 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042608
X-RAY DIFFRACTIONf_angle_d0.8743629
X-RAY DIFFRACTIONf_chiral_restr0.052402
X-RAY DIFFRACTIONf_plane_restr0.003386
X-RAY DIFFRACTIONf_dihedral_angle_d17.7321033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.18410.26131050.21382259236481
2.1841-2.28340.22881200.20532425254587
2.2834-2.40380.2651270.19862525265291
2.4038-2.55440.24161380.19592586272493
2.5544-2.75150.23141360.19832656279295
2.7515-3.02820.24441430.20822693283696
3.0282-3.4660.25611470.19922755290298
3.466-4.36510.21371300.17782791292198
4.3651-32.68850.2131510.19712892304397
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)
1-0.1119-0.0995-0.02620.79610.9311.1873-0.0296-0.0690.0371-0.0822-0.13330.0999-0.1119-0.09220.12570.14270.0015-0.01980.1844-0.05240.208313.9728-4.465117.5382
28.5107-2.148-7.60257.7984.25617.5786-0.3076-0.5544-0.01091.5873-0.22091.19610.8695-0.18740.54330.4516-0.16640.12850.5763-0.11740.3274.0713-12.091127.5015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 274
2X-RAY DIFFRACTION2chain B or chain CB2 - 12
3X-RAY DIFFRACTION2chain B or chain CC5 - 15

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