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- PDB-6rok: The crystal structure of a complex between the LlFpg protein, a T... -

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Basic information

Entry
Database: PDB / ID: 6rok
TitleThe crystal structure of a complex between the LlFpg protein, a THF-DNA and an inhibitor
Components
  • DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
  • Formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE / DNA glycosylase complex / inhibitor
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / 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 / MutM-like, N-terminal / N-terminal domain of MutM-like DNA repair proteins ...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 / 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
2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one / DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsCoste, F. / Goffinont, S. / Castaing, B.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights.
Authors: Rieux, C. / Goffinont, S. / Coste, F. / Tber, Z. / Cros, J. / Roy, V. / Guerin, M. / Gaudon, V. / Bourg, S. / Biela, A. / Aucagne, V. / Agrofoglio, L. / Garnier, N. / Castaing, B.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / refine / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase
D: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')
E: DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9777
Polymers39,5273
Non-polymers4504
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-21 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.633, 91.633, 141.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-621-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 31116.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Gene: mutM, fpg, NCDO763_0992 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A165FVI1, UniProt: P42371*PLUS, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 2 types, 2 molecules DE

#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')


Mass: 4054.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')


Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 316 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-5JL / 2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one


Mass: 200.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4OS2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, CITRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.95→47.84 Å / Num. obs: 44101 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.7
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3023 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.10_2142refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PM5

1pm5


Resolution: 1.95→47.839 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 4015 4.83 %
Rwork0.1675 79188 -
obs0.1689 83203 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.1 Å2 / Biso mean: 37.3477 Å2 / Biso min: 18.12 Å2
Refinement stepCycle: final / Resolution: 1.95→47.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 557 25 312 3053
Biso mean--48.52 43.13 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162856
X-RAY DIFFRACTIONf_angle_d1.4773953
X-RAY DIFFRACTIONf_chiral_restr0.079441
X-RAY DIFFRACTIONf_plane_restr0.009404
X-RAY DIFFRACTIONf_dihedral_angle_d17.3471630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9503-1.97320.34921160.35322641275796
1.9732-1.99730.33921410.32842797293899
1.9973-2.02260.28381280.3182669279799
2.0226-2.04920.37271260.30112774290099
2.0492-2.07730.33621260.30262710283698
2.0773-2.10690.28781750.2822694286999
2.1069-2.13840.2751290.25082735286499
2.1384-2.17180.22391360.23422726286299
2.1718-2.20740.23961340.2172744287899
2.2074-2.24550.27631450.20182733287899
2.2455-2.28630.23281740.1942729290399
2.2863-2.33030.19821190.18282733285299
2.3303-2.37780.21541360.17882742287899
2.3778-2.42950.21951280.16842737286599
2.4295-2.48610.20591400.17092784292499
2.4861-2.54820.19831650.17642677284299
2.5482-2.61710.21781700.180227362906100
2.6171-2.69410.20341450.18242745289099
2.6941-2.78110.22151490.18412734288399
2.7811-2.88050.23761490.180427352884100
2.8805-2.99580.20361240.18527582882100
2.9958-3.13210.20911180.166727762894100
3.1321-3.29720.1891240.162827662890100
3.2972-3.50370.14311410.137327712912100
3.5037-3.77410.1631340.138727442878100
3.7741-4.15370.1461160.12492759287599
4.1537-4.75430.14971360.10962705284198
4.7543-5.98810.14891410.13252718285999
5.9881-47.85290.17141500.14322616276695
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)
10.73350.0227-0.28991.1085-0.49023.00550.07110.01780.23-0.2298-0.02980.2792-0.0512-0.6553-0.00750.30220.0052-0.04460.3591-0.01380.3505-30.90413.155511.9361
24.26710.3939-0.94371.90920.30233.8744-0.1681-0.0052-0.20740.0270.06470.01880.4921-0.70320.14070.2591-0.0065-0.01920.3687-0.0140.2328-30.06842.417111.4007
32.0494-0.0182-0.61331.0368-0.24082.55830.0538-0.03270.0894-0.0073-0.0268-0.1232-0.19760.0556-0.02430.2523-0.01780.00070.1826-0.01980.2533-5.090611.065912.0337
41.00570.6278-0.45361.2956-0.72492.22080.0514-0.1424-0.06250.0796-0.0482-0.0060.0216-0.0862-0.00840.19610.0157-0.01520.2006-0.01990.2483-16.46821.616924.569
55.06121.5968-2.91253.3569-1.3062.6802-0.21980.1502-0.4232-0.3514-0.1245-0.39540.20030.17170.34950.34450.02370.00590.20650.0080.3513-9.9634-9.63522.139
62.60790.9630.42134.9095-0.37172.0401-0.22850.0672-0.2449-0.37020.2826-0.02680.582-0.3571-0.04440.4203-0.12360.0050.2782-0.01910.2802-24.4482-17.415619.481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 14 )D1 - 14
2X-RAY DIFFRACTION2chain 'E' and (resid 15 through 28 )E15 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 91 )A1 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 193 )A92 - 193
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 234 )A194 - 234
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 271 )A235 - 271

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