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- PDB-6tc6: Crystal structure of MutM from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 6tc6
TitleCrystal structure of MutM from Neisseria meningitidis
ComponentsFormamidopyrimidine-DNA glycosylaseDNA-formamidopyrimidine glycosylase
KeywordsHYDROLASE / MutM / Fpg/Nei / Neisseria meningitidis / BER / DNA repair
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. / Formamidopyrimidine-DNA glycosylase H2TH domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain ...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 / 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 / Ribosomal protein S13-like, H2TH
Similarity search - Domain/homology
Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis alpha522 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsSilhan, J. / Landova, B. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of Sciences17-21649Y Czech Republic
CitationJournal: Febs Lett. / Year: 2020
Title: Conformational changes of DNA repair glycosylase MutM triggered by DNA binding.
Authors: Landova, B. / Silhan, J.
History
DepositionNov 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase
C: Formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9364
Polymers61,8052
Non-polymers1312
Water0
1
A: Formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9682
Polymers30,9031
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9682
Polymers30,9031
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.378, 37.960, 110.303
Angle α, β, γ (deg.)90.000, 89.970, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 239 or resid 243 through 274))
21(chain C and (resid 1 through 185 or (resid 186...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 239 or resid 243 through 274))A1 - 239
121(chain A and (resid 1 through 239 or resid 243 through 274))A243 - 274
211(chain C and (resid 1 through 185 or (resid 186...C1 - 185
221(chain C and (resid 1 through 185 or (resid 186...C186
231(chain C and (resid 1 through 185 or (resid 186...C1 - 274
241(chain C and (resid 1 through 185 or (resid 186...C1 - 274
251(chain C and (resid 1 through 185 or (resid 186...C1 - 274
261(chain C and (resid 1 through 185 or (resid 186...C1 - 274

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Components

#1: Protein Formamidopyrimidine-DNA glycosylase / DNA-formamidopyrimidine glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase MutM / AP lyase MutM


Mass: 30902.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis alpha522 (bacteria)
Gene: mutM, fpg, NMALPHA522_0971 / Production host: Escherichia coli (E. coli)
References: UniProt: I4E596, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Bicine pH 8.5; 20% (w/v) PEG 6000 / PH range: 8.5 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.85→42.431 Å / Num. obs: 19597 / % possible obs: 96.4 % / Redundancy: 29.5 % / CC1/2: 0.844 / Net I/σ(I): 9.23
Reflection shellResolution: 2.85→2.952 Å / Num. unique obs: 1162 / CC1/2: 0.207

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→42.431 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.56
RfactorNum. reflection% reflection
Rfree0.298 606 5.34 %
Rwork0.2448 --
obs0.2476 11343 89.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.75 Å2 / Biso mean: 60.3284 Å2 / Biso min: 29.12 Å2
Refinement stepCycle: final / Resolution: 2.9→42.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 2 0 3968
Biso mean--85.12 --
Num. residues----502
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1526X-RAY DIFFRACTION9.032TORSIONAL
12C1526X-RAY DIFFRACTION9.032TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-3.19180.40021560.3391274793
3.1918-3.65340.36991340.2857260989
3.6534-4.6020.27831550.2285268090
4.602-42.4310.25581610.2116270188

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