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- PDB-3saw: MUTM Slanted complex 8 with R112A mutation -

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Basic information

Entry
Database: PDB / ID: 3saw
TitleMUTM Slanted complex 8 with R112A mutation
Components
  • 5'-D(*A*GP*GP*TP*AP*GP*AP*CP*AP*AP*GP*GP*AP*CP*GP*C)-3'
  • 5'-D(*TP*GP*CP*GP*TP*C*CP*TP*TP*GP*TP*(CX2)P*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 / oxidized purine nucleobase lesion 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: 2.35 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(*A*GP*GP*TP*AP*GP*AP*CP*AP*AP*GP*GP*AP*CP*GP*C)-3'
C: 5'-D(*TP*GP*CP*GP*TP*C*CP*TP*TP*GP*TP*(CX2)P*TP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4194
Polymers40,3543
Non-polymers651
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-15 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.295, 97.299, 102.736
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: 30497.213 Da / Num. of mol.: 1
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*AP*AP*GP*GP*AP*CP*GP*C)-3'


Mass: 4981.256 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*GP*CP*GP*TP*C*CP*TP*TP*GP*TP*(CX2)P*TP*AP*CP*C)-3'


Mass: 4875.248 Da / Num. of mol.: 1 / Source method: obtained synthetically
#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 / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 56.15 %
Crystal growTemperature: 273 K / pH: 7
Details: PEG 8K, SODIUM CACODYLATE, GLYCEROL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273K

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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: 2.3→50 Å / Num. obs: 20503 / % possible obs: 98.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.417 / % possible all: 99.6

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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: 2F5O

2f5o


Resolution: 2.35→26.3 Å / SU ML: 2.12 / σ(F): 0.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 895 4.89 %
Rwork0.185 --
obs0.187 18285 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.44 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 49.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0 Å2
2--3.442 Å20 Å2
3----2.332 Å2
Refinement stepCycle: LAST / Resolution: 2.35→26.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 431 1 98 2470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072466
X-RAY DIFFRACTIONf_angle_d1.1113430
X-RAY DIFFRACTIONf_dihedral_angle_d20.19937
X-RAY DIFFRACTIONf_chiral_restr0.065386
X-RAY DIFFRACTIONf_plane_restr0.005371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.351-2.4980.2941510.2192571X-RAY DIFFRACTION84
2.498-2.690.3081510.2092800X-RAY DIFFRACTION93
2.69-2.9610.2351380.2022892X-RAY DIFFRACTION94
2.961-3.3880.231590.1892961X-RAY DIFFRACTION96
3.388-4.2660.2221410.1653045X-RAY DIFFRACTION97
4.266-26.3020.2051550.1693121X-RAY DIFFRACTION95
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)
1-0.1316-0.12120.07641.5909-1.15120.9060.0071-0.0681-0.0003-0.0059-0.1434-0.12340.04330.0720.10560.0620.01110.0040.10360.06590.0823-14.0253.524417.1127
26.8608-4.68162.81399.3619-1.04721.8619-0.35020.38690.57491.3481-0.2303-1.7702-0.0356-0.26050.52960.242-0.0513-0.16690.28740.15270.4606-5.225261.396427.0032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B OR CHAIN C

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