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- PDB-1pm5: Crystal structure of wild type Lactococcus lactis Fpg complexed t... -

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Basic information

Entry
Database: PDB / ID: 1pm5
TitleCrystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran 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 repair / Fpg / MutM / abasic site / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPereira de Jesus-Tran, K. / Serre, L. / Zelwer, C. / Castaing, B.
Citation
Journal: Nucleic Acids Res. / Year: 2005
Title: Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA.
Authors: Pereira de Jesus, K. / Serre, L. / Zelwer, C. / Castaing, B.
#1: Journal: Embo J. / Year: 2002
Title: Crystal structure of the Lactococcus lactis Formamidopyrimidine DNA glycosylase bound to an abasic site analogue-containing DNA
Authors: Serre, L. / Pereira de Jesus, K. / Boiteux, S. / Zelwer, C. / Castaing, B.
History
DepositionJun 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The author maintains that the Asp137 is an error in the sequence database. This residue ...sequence The author maintains that the Asp137 is an error in the sequence database. This residue does not exist.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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')
A: Formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8687
Polymers39,5273
Non-polymers3424
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.784, 91.784, 141.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsthe biological assembly corresponds to one Fpg molecule and one DNA duplex

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Components

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DNA chain , 2 types, 2 molecules DE

#1: 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 / Details: synyhetic
#2: 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 / Details: synthetic

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Protein , 1 types, 1 molecules A

#3: Protein Formamidopyrimidine-DNA glycosylase / 3.2.2.23 / FAPY-DNA glycosylase


Mass: 31116.217 Da / Num. of mol.: 1 / Fragment: Fpg
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Species: Lactococcus lactis / Strain: subsp. cremoris / Gene: MUTM OR FPG / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase

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Non-polymers , 3 types, 310 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: citrate, hepes, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1citrate11
2hepes11
3glycerol11
4water11
5citrate12
6glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2003
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→77 Å / Num. all: 43785 / Num. obs: 43717 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 29.042 Å2 / Rsym value: 0.045 / Net I/σ(I): 10.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4 / Rsym value: 0.147 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSVERSION 1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NNJ

1nnj


Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2158 -RANDOM
Rwork0.1962 ---
all-44852 --
obs-43716 97.5 %-
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 557 19 306 3042
LS refinement shellResolution: 1.95→1.97 Å /
RfactorNum. reflection
Rfree0.2216 24
Rwork0.1871 -

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