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- PDB-3sar: MUTM Slanted complex 1 -

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Basic information

Entry
Database: PDB / ID: 3sar
TitleMUTM Slanted complex 1
Components
  • 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'
  • 5'-D(*TP*GP*C*GP*TP*CP*CP*AP*GP*GP*TP*(CX2) P*TP*AP*CP*C)-3'
  • Formamidopyrimidine-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: 1.95 Å
AuthorsBanerjee, A. / Qi, Y. / Spong, M.C. / 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 / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _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: Formamidopyrimidine-DNA glycosylase
C: 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'
D: 5'-D(*TP*GP*C*GP*TP*CP*CP*AP*GP*GP*TP*(CX2) P*TP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8758
Polymers40,4413
Non-polymers4345
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-24 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.253, 96.126, 103.480
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 Formamidopyrimidine-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

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DNA
#3: DNA chain 5'-D(*TP*GP*C*GP*TP*CP*CP*AP*GP*GP*TP*(CX2) P*TP*AP*CP*C)-3'


Mass: 4909.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DNA

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Non-polymers , 3 types, 206 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 298 K / 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: NSLS / Beamline: X25 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 33367 / % possible obs: 98.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.355 / % possible all: 87.6

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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: 2F5N

2f5n


Resolution: 1.95→45.56 Å / SU ML: 1.63 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1594 4.95 %
Rwork0.194 --
obs0.196 32173 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.18 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 47.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.313 Å20 Å2-0 Å2
2--1.118 Å20 Å2
3----2.553 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 551 25 201 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072649
X-RAY DIFFRACTIONf_angle_d1.0663694
X-RAY DIFFRACTIONf_dihedral_angle_d20.5341023
X-RAY DIFFRACTIONf_chiral_restr0.062411
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0070.247920.2252146X-RAY DIFFRACTION74
2.007-2.0790.2831230.2012606X-RAY DIFFRACTION89
2.079-2.1620.211720.1922693X-RAY DIFFRACTION94
2.162-2.2610.2241350.1882774X-RAY DIFFRACTION95
2.261-2.380.2281450.1862811X-RAY DIFFRACTION97
2.38-2.5290.2581340.1952850X-RAY DIFFRACTION97
2.529-2.7240.2151560.1992837X-RAY DIFFRACTION98
2.724-2.9990.231430.2012908X-RAY DIFFRACTION99
2.999-3.4320.2291620.1942914X-RAY DIFFRACTION99
3.432-4.3240.1931680.1752940X-RAY DIFFRACTION99
4.324-45.5720.2191640.1923100X-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)
1-0.18280.04190.02270.9194-1.06521.3002-0.0087-0.0654-0.0601-0.111-0.1518-0.09260.1290.10540.12450.17050.01690.0230.19290.0580.2118-13.847452.95917.4199
21.1470.70421.50712.4661-0.84041.765-0.5574-0.91460.16611.08280.0107-1.0051-0.86170.35010.51720.6594-0.0627-0.11510.86890.06320.5325-4.994961.657728.5315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN C OR CHAIN D

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