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- PDB-3a46: Crystal structure of MvNei1/THF complex -

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Basic information

Entry
Database: PDB / ID: 3a46
TitleCrystal structure of MvNei1/THF complex
Components
  • (DNA) x 2
  • Formamidopyrimidine-DNA glycosylaseDNA-formamidopyrimidine glycosylase
KeywordsHYDROLASE / helix two turns helix / zinc-less finger / THF / DNA damage / DNA repair / DNA-binding / Glycosidase / Lyase / Multifunctional enzyme
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 C-terminal domain / 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 C-terminal domain / 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) / Probable formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsImamura, K. / Wallace, S. / Doublie, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Characterization of a Viral NEIL1 Ortholog Unliganded and Bound to Abasic Site-containing DNA
Authors: Imamura, K. / Wallace, S.S. / Doublie, S.
History
DepositionJul 1, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Formamidopyrimidine-DNA glycosylase
C: DNA
D: DNA
E: DNA
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1897
Polymers83,0976
Non-polymers921
Water7,512417
1
A: Formamidopyrimidine-DNA glycosylase
C: DNA
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6414
Polymers41,5493
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-20 kcal/mol
Surface area16220 Å2
MethodPISA
2
B: Formamidopyrimidine-DNA glycosylase
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)41,5493
Polymers41,5493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-18 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.513, 121.462, 80.510
Angle α, β, γ (deg.)90.000, 95.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Formamidopyrimidine-DNA glycosylase / DNA-formamidopyrimidine glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase / AP lyase / Endonuclease VIII / MvNei1


Mass: 33753.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: L315 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys
References: UniProt: Q5UQ00, DNA-formamidopyrimidine glycosylase
#2: DNA chain DNA /


Mass: 4016.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Nucleotide synthesis
#3: DNA chain DNA /


Mass: 3778.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Nucleotide synthesis
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, 100mM bis-Tris, pH6.0-6.3, 150mM magnesium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2bis-TrisBis-tris methane11
3magnesium nitrate11
4HOH11
5PEG335012
6bis-TrisBis-tris methane12
7magnesium nitrate12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. all: 38298 / Num. obs: 38069 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A45

3a45


Resolution: 2.2→35 Å / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3574 9.3 %RANDOM
Rwork0.213 ---
all-38229 --
obs-35872 93.7 %-
Solvent computationBsol: 58.124 Å2
Displacement parametersBiso max: 79.74 Å2 / Biso mean: 31.26 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1-2.894 Å20 Å21.046 Å2
2---5.739 Å20 Å2
3---2.845 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4754 1032 6 417 6209
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.242
X-RAY DIFFRACTIONc_mcbond_it1.5151.5
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_mcangle_it2.5182
X-RAY DIFFRACTIONc_scangle_it3.2272.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.033
RfactorNum. reflection% reflection
Rfree0.578 251 -
Rwork0.52 --
obs-2484 52.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5gol_xplor_paramgol_xplor_top

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