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- PDB-3vk7: Crystal structure of DNA-glycosylase bound to DNA containing 5-Hy... -

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Basic information

Entry
Database: PDB / ID: 3vk7
TitleCrystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3')
  • Probable formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / hNEIL1 ortholog / DNA LESION / 5-Hydroxyuracil / Zincless finger / DNA binding / 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 C-terminal domain / 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 C-terminal domain / 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
FORMIC ACID / DNA / DNA (> 10) / Probable formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsImamura, K. / Averill, A. / Wallace, S.S. / Doublie, S.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA
Authors: Imamura, K. / Averill, A. / Wallace, S.S. / Doublie, S.
#1: Journal: 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
DepositionNov 10, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 8, 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_ncs_dom_lim / 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_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 / _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: Probable formamidopyrimidine-DNA glycosylase
B: Probable formamidopyrimidine-DNA glycosylase
C: DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3')
E: DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1778
Polymers85,0856
Non-polymers922
Water8,215456
1
A: Probable formamidopyrimidine-DNA glycosylase
C: DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5894
Polymers42,5433
Non-polymers461
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-21 kcal/mol
Surface area16340 Å2
MethodPISA
2
B: Probable formamidopyrimidine-DNA glycosylase
E: DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5894
Polymers42,5433
Non-polymers461
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-20 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.703, 121.594, 81.121
Angle α, β, γ (deg.)90.000, 95.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLUchain A and (resseq 7:200 )AA7 - 2007 - 200
21VALVALGLUGLUchain B and (resseq 7:200 )BB7 - 2007 - 200
12SERSERILEILEchain A and (resseq 230:270 )AA230 - 270230 - 270
22SERSERILEILEchain B and (resseq 230:270 )BB230 - 270230 - 270

NCS ensembles :
ID
1
2

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Components

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


Mass: 34581.367 Da / Num. of mol.: 2 / Mutation: E3Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_L315 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys
References: UniProt: Q5UQ00, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3')


Mass: 4056.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: complementary DNA
#3: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3904.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA containing 5-hydroxyuracil
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.29 Å3/Da / Density % sol: 46.31 % / Mosaicity: 0.561 °
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG 3350, HCOONa, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2010 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 45100 / Num. obs: 41763 / % possible obs: 92.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.117 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.182.70.23244390.575198.9
2.18-2.262.80.21544110.973198.5
2.26-2.372.60.18742320.737193.7
2.37-2.492.80.1444630.775199.1
2.49-2.652.90.11644590.787199.2
2.65-2.852.90.10244981.016199.4
2.85-3.142.80.08544491.372199.1
3.14-3.592.80.0735241.644178.3
3.59-4.522.70.05228181.816162.1
4.52-502.90.04844701.792197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3A46

3a46


Resolution: 2.1→28.296 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7917 / SU ML: 1.17 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 3770 9.27 %from starting model 3A46
Rwork0.2128 ---
obs0.2179 40659 91.11 %-
all-44626 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.299 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 85.98 Å2 / Biso mean: 25.4534 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.2251 Å20 Å2-1.5255 Å2
2---3.0974 Å2-0 Å2
3---5.3225 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 1056 6 456 6241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056116
X-RAY DIFFRACTIONf_angle_d0.9898485
X-RAY DIFFRACTIONf_chiral_restr0.067889
X-RAY DIFFRACTIONf_plane_restr0.004890
X-RAY DIFFRACTIONf_dihedral_angle_d20.2242354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1577X-RAY DIFFRACTIONPOSITIONAL0.023
12B1577X-RAY DIFFRACTIONPOSITIONAL0.023
21A337X-RAY DIFFRACTIONPOSITIONAL0.019
22B337X-RAY DIFFRACTIONPOSITIONAL0.019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12660.35881390.23871442158197
2.1266-2.15450.29721430.24271396153995
2.1545-2.18410.34061740.23821404157894
2.1841-2.21520.29421090.23111446155594
2.2152-2.24830.2509430.25411474151793
2.2483-2.28340.3182960.2711277137382
2.2834-2.32080.3031120.23591376148892
2.3208-2.36080.30891660.22351404157095
2.3608-2.40370.27311490.21691441159097
2.4037-2.44990.30431660.21961467163398
2.4499-2.49990.29431620.22341473163598
2.4999-2.55420.2791470.21341441158898
2.5542-2.61360.26361660.20261479164598
2.6136-2.67890.29911400.2011472161299
2.6789-2.75130.2621620.22171458162099
2.7513-2.83220.29881630.22351513167699
2.8322-2.92350.31731700.22931433160399
2.9235-3.02790.28621660.219514991665100
3.0279-3.1490.22971730.19811436160999
3.149-3.29210.26391710.19991500167199
3.2921-3.46540.22681510.17791391154294
3.4654-3.68210.2178220.162831834020
3.6821-3.96560.1547530.181448754032
3.9656-4.36340.21551360.17751410154694
4.3634-4.99180.21351570.17171486164399
4.9918-6.27780.22551790.189814751654100
6.2778-28.29850.21831550.19351491164697

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