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Basic information

Entry
Database: PDB / ID: 4nrw
TitleMvNei1-G86D
Components
  • 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3'
  • 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
  • formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE / LYASE/DNA / zinc-less finger domain / DNA glycosylase / helix two-turns helix motif / THF / DNA lyase / LYASE-DNA complex
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 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.845 Å
AuthorsPrakash, A. / Doublie, S.
CitationJournal: Dna Repair / Year: 2014
Title: Genome and cancer single nucleotide polymorphisms of the human NEIL1 DNA glycosylase: Activity, structure, and the effect of editing.
Authors: Prakash, A. / Carroll, B.L. / Sweasy, J.B. / Wallace, S.S. / Doublie, S.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Sep 20, 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
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

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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: 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3'
E: 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
F: 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)84,6096
Polymers84,6096
Non-polymers00
Water1448
1
A: formamidopyrimidine-DNA glycosylase
C: 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)42,3043
Polymers42,3043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-20 kcal/mol
Surface area16230 Å2
MethodPISA
2
B: formamidopyrimidine-DNA glycosylase
E: 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
F: 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)42,3043
Polymers42,3043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-19 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.401, 121.682, 79.993
Angle α, β, γ (deg.)90.00, 95.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain E
13chain D
23chain F

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
11PROPROGLNGLNchain AAA2 - 2861 - 285
21PROPROGLNGLNchain BBB2 - 2861 - 285
12DGDGDGDGchain CCC1 - 131 - 13
22DGDGDGDGchain EEE1 - 131 - 13
13DCDCDCDCchain DDD14 - 261 - 13
23DCDCDCDCchain FFF14 - 261 - 13

NCS ensembles :
ID
1
2
3

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Components

#1: Protein formamidopyrimidine-DNA glycosylase / Nei1 (MvNei1) DNA glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 34509.191 Da / Num. of mol.: 2 / Mutation: G86D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: Endonuclease VIII (nei) 1, MIMI_L315 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)PlysS
References: UniProt: Q5UQ00, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'


Mass: 4016.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: complementary DNA strand
#3: DNA chain 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3'


Mass: 3778.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: furan-containing DNA strand
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 4% w/v PEG8000, 0.125 M potassium chloride, 0.05 M magnesium sulfate, 100 mM MES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2013
RadiationMonochromator: MAR mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.845→15 Å / Num. obs: 17340 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.185 / Χ2: 1.064 / Net I/σ(I): 4.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.845-2.953.10.52316960.813198.7
2.95-3.073.20.40217240.936198.2
3.07-3.213.40.30517251.053199.4
3.21-3.373.50.23217411.177199.1
3.37-3.583.60.20317531.196199.3
3.58-3.853.60.16417141.196199
3.85-4.233.60.16317341.196199.1
4.23-4.833.70.1317421.01199.1
4.83-6.023.70.14317340.99199.1
6.02-153.70.11417771.008199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.85 Å14.97 Å
Translation2.85 Å14.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A46

3a46


Resolution: 2.845→14.966 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7381 / SU ML: 0.46 / σ(F): 1.37 / Phase error: 32.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3145 1758 10.15 %
Rwork0.2599 --
obs0.2653 17318 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.52 Å2 / Biso mean: 29.6461 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.845→14.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 1032 0 8 5722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025960
X-RAY DIFFRACTIONf_angle_d0.6148257
X-RAY DIFFRACTIONf_chiral_restr0.041872
X-RAY DIFFRACTIONf_plane_restr0.003871
X-RAY DIFFRACTIONf_dihedral_angle_d15.5572293
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2596X-RAY DIFFRACTION7.536TORSIONAL
12B2596X-RAY DIFFRACTION7.536TORSIONAL
21C252X-RAY DIFFRACTION7.536TORSIONAL
22E252X-RAY DIFFRACTION7.536TORSIONAL
31D226X-RAY DIFFRACTION7.536TORSIONAL
32F226X-RAY DIFFRACTION7.536TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.845-2.92190.41251530.33351132128598
2.9219-3.00720.35911250.32611207133299
3.0072-3.10340.35811340.32731192132698
3.1034-3.21330.33251440.30481181132599
3.2133-3.34060.32611110.2761205131699
3.3406-3.49080.32071350.27081195133099
3.4908-3.67230.30631390.24811211135099
3.6723-3.89850.35641380.24681202134099
3.8985-4.19340.28561240.23991192131699
4.1934-4.60420.26991250.23081209133499
4.6042-5.24520.27991450.23271195134099
5.2452-6.51630.3051490.247212241373100
6.5163-14.96670.27321360.22221215135199
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)
11.2139-0.01480.02831.08010.18430.4165-0.00470.0393-0.0143-0.13420.0411-0.033-0.0666-0.00820.00340.175-0.0017-0.00550.1345-0.0090.0799-8.74380.568115.2205
20.9328-0.33930.24571.9058-0.59670.52440.01390.10470.087-0.1217-0.06570.09170.1185-0.0217-0.00420.1753-0.02850.02450.1530.01120.1435-11.14818.854775.4367
30.17860.2090.15590.28590.18810.11670.0829-0.2157-0.20180.2983-0.1354-0.1521-0.21330.1263-0.01070.1977-0.02950.0560.5634-0.04110.3778-5.3344-8.5676137.4811
40.10260.04790.41470.04560.1831.99460.0051-0.3401-0.3921-0.07490.0049-0.10270.5314-0.5569-0.28090.1879-0.07590.04230.3787-0.1040.4067-25.6-7.0861130.4792
52.4777-0.13321.72912.17231.57612.5437-0.229-0.916-0.04040.1538-0.17380.67350.2054-0.3195-0.43140.2556-0.0324-0.05040.4740.14810.5694-23.5661-12.2666134.2221
60.189-0.25210.18610.5208-0.26770.2107-0.3112-0.07940.31530.19690.01340.1261-0.04980.198-0.02210.2744-0.0584-0.05040.7503-0.10690.7611-14.641528.717497.3204
70.445-0.334-0.50030.34450.1141.3735-0.0452-0.48610.4589-0.04420.0006-0.0521-0.60970.28720.15290.2904-0.0791-0.05260.3196-0.00180.42145.663427.043590.5099
80.28340.0943-0.34670.77490.13520.53570.0898-0.42390.00140.2712-0.1085-0.5814-0.1480.4706-0.3284-0.0532-0.1033-0.06580.6346-0.13080.95233.483332.413994.2263
91.0002-0.39450.72053.5977-0.73190.5789-0.2299-0.70860.29780.6056-0.06290.74710.0217-0.53190.06390.17-0.10550.11850.8646-0.22010.7005-17.360822.907993.4747
101.0438-0.03620.76520.85670.21830.9371-0.0803-0.10560.07620.9108-0.1541-0.6130.00450.2432-0.0394-0.0329-0.2004-0.40310.5290.18350.6786-2.5786-2.9646133.3387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 286 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 286 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 6 )C0
4X-RAY DIFFRACTION4chain 'C' and (resid 7 through 13 )C0
5X-RAY DIFFRACTION5chain 'D' and (resid 14 through 19 )D0
6X-RAY DIFFRACTION6chain 'E' and (resid 1 through 6 )E0
7X-RAY DIFFRACTION7chain 'E' and (resid 7 through 13 )E0
8X-RAY DIFFRACTION8chain 'F' and (resid 14 through 19 )F0
9X-RAY DIFFRACTION9chain 'F' and (resid 21 through 26 )F0
10X-RAY DIFFRACTION10chain 'D' and (resid 21 through 26 )D0

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