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- PDB-1nnj: Crystal structure Complex between the Lactococcus lactis Fpg and ... -

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Basic information

Entry
Database: PDB / ID: 1nnj
TitleCrystal structure Complex between the Lactococcus lactis Fpg and an abasic site containing DNA
Components
  • 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3'
  • 5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'
  • Formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE / DNA repair / Fpg / MutM / abasic site
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 / 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 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSerre, L. / Pereira de Jesus, K. / Boiteux, S. / 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: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and primary X-ray crystallographic studies of a complex between the Lactococcus lactis Fpg DNA-repair enzyme and an abasic site containing DNA
Authors: Pereira de Jesus, K. / Serre, L. / Hervouet, N. / Bouckson-Castaing, V. / Zelwer, C. / Castaing, B.
History
DepositionJan 14, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3'
E: 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)39,6946
Polymers39,4453
Non-polymers2503
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.150, 92.150, 142.530
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-389-

HOH

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Components

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DNA chain , 2 types, 2 molecules DE

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


Mass: 4012.577 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 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

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Protein , 1 types, 1 molecules A

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


Mass: 31076.154 Da / Num. of mol.: 1 / Mutation: P1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: MUTM / Plasmid: pmal-c / Production host: Escherichia coli (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase

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Non-polymers , 3 types, 230 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.63 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: citrate, Hepes, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1citrate11
2Hepes11
3Glycerol11
4Glycerol12
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
21.4 Msodium citrate1reservoir
30.1 Msodium HEPES1reservoirpH7.5
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2002
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→44 Å / Num. all: 56976 / Num. obs: 56858 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.074 / Net I/σ(I): 6.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7923 / Rsym value: 0.627 / % possible all: 94.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 44 Å / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Rmerge(I) obs: 0.627

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KFV

1kfv


Resolution: 1.9→35 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2425 -RANDOM
Rwork0.215 ---
all-48742 --
obs-48703 99.9 %-
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 554 13 227 2942
LS refinement shellResolution: 1.9→1.91 Å /
RfactorNum. reflection
Rfree0.29 102
Rwork0.266 -
Refinement
*PLUS
Lowest resolution: 35 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.21
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.29

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