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- PDB-4pcz: Crystal structure of a complex between R247G LlFPG mutant and a T... -

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Basic information

Entry
Database: PDB / ID: 4pcz
TitleCrystal structure of a complex between R247G LlFPG mutant and a THF containing DNA
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 / DNA glycosylase / THF / Hydrolase-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 / 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. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / 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. / 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) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCoste, F. / Castaing, B.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Authors: Biela, A. / Coste, F. / Culard, F. / Guerin, M. / Goffinont, S. / Gasteiger, K. / Ciesla, J. / Winczura, A. / Kazimierczuk, Z. / Gasparutto, D. / Carell, T. / Tudek, B. / Castaing, B.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _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
B: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')
C: 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)39,5845
Polymers39,4273
Non-polymers1582
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-22 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.723, 91.723, 142.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-463-

HOH

31A-470-

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: 31016.072 Da / Num. of mol.: 1 / Mutation: R247G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Gene: mutM, fpg / Production host: Escherichia coli (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase

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DNA chain , 2 types, 2 molecules BC

#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 , 3 types, 455 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.7→47.94 Å / Num. obs: 65739 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.6 / % possible all: 88.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PM5

1pm5


Resolution: 1.7→47.94 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 6213 5.14 %Random selection
Rwork0.1567 ---
obs0.158 120884 94.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 557 7 453 3172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192881
X-RAY DIFFRACTIONf_angle_d1.8254004
X-RAY DIFFRACTIONf_dihedral_angle_d18.5821155
X-RAY DIFFRACTIONf_chiral_restr0.101449
X-RAY DIFFRACTIONf_plane_restr0.01412
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)
10.1103-0.1131-0.03470.1904-0.05650.2983-0.0996-0.06680.2656-0.07230.07020.1154-0.2458-0.1218-00.216-0.0080.01590.2065-0.01260.24212.8143182.3308158.8573
20.8667-0.36810.35370.5869-0.39310.53030.1121-0.0894-0.1188-0.0659-0.03730.1420.1312-0.02850.02380.1959-0.0363-0.01190.11890.01470.18624.8238167.1853156.0713
30.256-0.27860.17410.23970.08420.43060.05420.1271-0.001-0.06860.03540.054-0.05440.0719-00.2159-0.0044-0.01380.19850.03030.19437.1786175.6347146.3559
40.38640.294-0.00930.34420.14140.06940.0356-0.1704-0.03890.1046-0.04280.04640.1513-0.012100.2481-0.00190.02340.19760.01160.190311.1063173.4832169.6208
51.02050.4876-0.51710.63510.24280.83830.0066-0.1129-0.0426-0.027-0.005-0.0749-0.09830.204-00.2082-0.02590.0110.1888-0.00490.209723.0028189.785173.1233
60.71770.0333-0.25350.6262-0.07990.0719-0.18970.02360.2391-0.1029-0.10420.2397-0.2298-0.1503-00.2666-0.0056-0.00750.1421-0.01470.237710.0326192.4946165.6181
70.1743-0.0584-0.05150.3262-0.08170.0928-0.21740.21790.1923-0.42280.12660.3397-0.3872-0.0863-0.04110.4585-0.076-0.03940.19420.0220.295618.1472202.9353158.9566
80.1146-0.05320.10290.1237-0.08710.1175-0.23860.0922-0.0493-0.10110.3212-0.0793-0.31640.37650.00430.3185-0.09320.03550.2527-0.02290.244827.9021197.9322163.295
90.09580.22330.06840.36770.1730.21290.0413-0.0512-0.0523-0.12840.0113-0.16470.03380.265400.26030.00710.05010.27160.01920.257830.8211179.7606154.4696
100.660.1571-0.00990.1807-0.09740.047-0.11120.2118-0.0696-0.01240.1351-0.0611-0.11460.59590.03110.2757-0.01780.00810.33770.01940.228430.0725180.9069153.6371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 141 )
5X-RAY DIFFRACTION5chain 'A' and (resid 142 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 230 )
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 251 )
8X-RAY DIFFRACTION8chain 'A' and (resid 252 through 271 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 14 )
10X-RAY DIFFRACTION10chain 'C' and (resid 15 through 28 )

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