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- PDB-3uf7: Co-crystal structure of Escherichia coli uracil-DNA glycosylase a... -

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Basic information

Entry
Database: PDB / ID: 3uf7
TitleCo-crystal structure of Escherichia coli uracil-DNA glycosylase and a C-terminal fragement of the single-stranded DNA-binding protein
Components
  • Single-stranded DNA-binding protein
  • Uracil-DNA glycosylase
KeywordsHYDROLASE / Glycosylase / SSB C-terminal / Base excision repair
Function / homology
Function and homology information


single-stranded DNA-binding protein complex / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair ...single-stranded DNA-binding protein complex / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E ...Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Nucleic acid-binding, OB-fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Single-stranded DNA-binding protein / Uracil-DNA glycosylase / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsGeorge, N.P. / Liban, T.J. / Reyes-Lamothe, R. / Keck, J.L.
CitationJournal: To be Published
Title: Identification of the SSB-interaction platform of Escherichia coli uracil-DNA glycosylase
Authors: George, N.P. / Liban, T.J. / Reyes-Lamothe, R. / Keck, J.L.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Single-stranded DNA-binding protein
C: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4097
Polymers29,0253
Non-polymers3844
Water5,603311
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-50 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.204, 118.204, 47.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 26796.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. MG1655 / Gene: b2580, JW2564, ung / Plasmid: pET28, pNPG028 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P12295, uracil-DNA glycosylase
#2: Protein/peptide Single-stranded DNA-binding protein / SSB


Mass: 1114.182 Da / Num. of mol.: 2 / Fragment: UNP residues 170-178 / Source method: obtained synthetically / Details: E. coli SSB C-terminal peptide / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q0T9Z4, UniProt: P0AGE0*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4-1.8M NH4SO4, 0.01M MgCl2 & 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 15, 2008
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 99762 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.048 / Χ2: 1.006 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.222.40.41742441.002183.9
1.22-1.242.80.42247121.024193.1
1.24-1.273.30.43149470.999198.6
1.27-1.293.80.38750461199.7
1.29-1.324.30.36150551.0821100
1.32-1.354.60.3250701.0711100
1.35-1.394.90.2851021.0141100
1.39-1.4250.22950091.0431100
1.42-1.4650.17250541.0541100
1.46-1.5150.1450571.0781100
1.51-1.5750.11950831.1281100
1.57-1.6350.10150781.1211100
1.63-1.75.10.08550661.1491100
1.7-1.795.10.06550711.1481100
1.79-1.95.10.0550571.032199.8
1.9-2.0550.04150881.141199.7
2.05-2.265.10.03450750.93199.5
2.26-2.585.10.03250730.849199.4
2.58-3.266.20.04550380.793197.9
3.26-308.40.04548370.748192

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LQG

1lqg


Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.1568 / WRfactor Rwork: 0.1384 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9199 / SU B: 0.867 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0294 / SU Rfree: 0.0292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1561 4982 5 %RANDOM
Rwork0.1392 ---
obs0.1401 99629 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 225.81 Å2 / Biso mean: 22.0131 Å2 / Biso min: 10.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 20 311 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022038
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9472809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8755266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98323.9898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17115331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2611511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211596
X-RAY DIFFRACTIONr_rigid_bond_restr4.27332038
X-RAY DIFFRACTIONr_sphericity_free53.609568
X-RAY DIFFRACTIONr_sphericity_bonded20.4952214
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 311 -
Rwork0.318 5985 -
all-6296 -
obs--86.08 %

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