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- PDB-6tc9: Crystal structure of MutM from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 6tc9
TitleCrystal structure of MutM from Neisseria meningitidis
Components
  • DNA
  • DNA containing abasic site analogue
  • Formamidopyrimidine-DNA glycosylase
KeywordsDNA BINDING PROTEIN / MutM / Fpg/Nei / Neisseria meningitidis / BER / DNA repair
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 / 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
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis alpha522 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.175 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 1.0Sep 16, 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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA containing abasic site analogue
G: DNA containing abasic site analogue
A: Formamidopyrimidine-DNA glycosylase
B: DNA
C: Formamidopyrimidine-DNA glycosylase
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7869
Polymers78,6306
Non-polymers1553
Water1,06359
1
D: DNA containing abasic site analogue
A: Formamidopyrimidine-DNA glycosylase
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3814
Polymers39,3153
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-16 kcal/mol
Surface area15970 Å2
MethodPISA
2
G: DNA containing abasic site analogue
C: Formamidopyrimidine-DNA glycosylase
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4055
Polymers39,3153
Non-polymers902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-21 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.770, 80.380, 83.620
Angle α, β, γ (deg.)90.000, 89.950, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 123 or resid 126...
21(chain C and (resid 2 through 31 or resid 33...
12chain B
22chain F
13chain D
23chain G

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLUGLU(chain A and (resid 2 through 123 or resid 126...AC2 - 1232 - 123
121GLUGLUPHEPHE(chain A and (resid 2 through 123 or resid 126...AC126 - 236126 - 236
131PROPROLYSLYS(chain A and (resid 2 through 123 or resid 126...AC2 - 2752 - 275
141PROPROLYSLYS(chain A and (resid 2 through 123 or resid 126...AC2 - 2752 - 275
151PROPROLYSLYS(chain A and (resid 2 through 123 or resid 126...AC2 - 2752 - 275
161PROPROLYSLYS(chain A and (resid 2 through 123 or resid 126...AC2 - 2752 - 275
171PROPROLYSLYS(chain A and (resid 2 through 123 or resid 126...AC2 - 2752 - 275
181PROPROLYSLYS(chain A and (resid 2 through 123 or resid 126...AC2 - 2752 - 275
191PROPROLYSLYS(chain A and (resid 2 through 123 or resid 126...AC2 - 2752 - 275
211PROPROLEULEU(chain C and (resid 2 through 31 or resid 33...CE2 - 312 - 31
221LEULEUILEILE(chain C and (resid 2 through 31 or resid 33...CE33 - 6233 - 62
231ARGARGARGARG(chain C and (resid 2 through 31 or resid 33...CE6363
241PROPROLYSLYS(chain C and (resid 2 through 31 or resid 33...CE2 - 2752 - 275
251PROPROLYSLYS(chain C and (resid 2 through 31 or resid 33...CE2 - 2752 - 275
261PROPROLYSLYS(chain C and (resid 2 through 31 or resid 33...CE2 - 2752 - 275
271PROPROLYSLYS(chain C and (resid 2 through 31 or resid 33...CE2 - 2752 - 275
112DADADCDCchain BBD1 - 141 - 14
212DADADCDCchain FFF1 - 141 - 14
113DTDTDCDCchain DDA3 - 143 - 14
213DTDTDCDCchain GGB3 - 143 - 14

NCS ensembles :
ID
1
2
3

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Components

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DNA chain , 2 types, 4 molecules DGBF

#1: DNA chain DNA containing abasic site analogue


Mass: 4082.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA


Mass: 4329.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AC

#2: Protein Formamidopyrimidine-DNA 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

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Non-polymers , 3 types, 62 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris-HCl pH = 8.5, 200 mM Magnesium acetate,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795, 1.0389
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.03891
ReflectionResolution: 2.175→36.223 Å / Num. obs: 44999 / % possible obs: 98.6 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.083 / Net I/σ(I): 7.63
Reflection shellResolution: 2.175→2.253 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 4371 / CC1/2: 0.856 / Rrim(I) all: 0.7124 / % possible all: 95.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2-3472refinement
XSCALEdata processing
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TC6

6tc6


Resolution: 2.175→36.223 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2809 2246 5 %
Rwork0.238 --
obs0.2401 44909 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.19 Å2 / Biso mean: 72.4471 Å2 / Biso min: 31.43 Å2
Refinement stepCycle: final / Resolution: 2.175→36.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 1036 3 59 5173
Biso mean--64.29 67.3 -
Num. residues----570
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1562X-RAY DIFFRACTION7.174TORSIONAL
12C1562X-RAY DIFFRACTION7.174TORSIONAL
21B272X-RAY DIFFRACTION7.174TORSIONAL
22F272X-RAY DIFFRACTION7.174TORSIONAL
31D236X-RAY DIFFRACTION7.174TORSIONAL
32G236X-RAY DIFFRACTION7.174TORSIONAL
Refinement TLS params.Method: refined / Origin x: 42.6938 Å / Origin y: 1.1627 Å / Origin z: 20.8958 Å
111213212223313233
T0.2815 Å20.0008 Å2-0.0002 Å2-0.4497 Å20.0064 Å2--0.2819 Å2
L0.9088 °20.0157 °2-0.003 °2-0.8358 °20.3036 °2--4.2576 °2
S0.3026 Å °0.0075 Å °-0.0081 Å °-0.0118 Å °-0.4264 Å °-0.1751 Å °-0.0236 Å °-0.6413 Å °0.0472 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD3 - 14
2X-RAY DIFFRACTION1allG3 - 14
3X-RAY DIFFRACTION1allA2 - 275
4X-RAY DIFFRACTION1allB1 - 14
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allC2 - 275
7X-RAY DIFFRACTION1allF1 - 14
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allJ1 - 59
10X-RAY DIFFRACTION1allK1

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