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- PDB-4zbz: Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free fo... -

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Basic information

Entry
Database: PDB / ID: 4zbz
TitleFamily 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / Uracil-DNA glycosylase / DNA repair
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding
Similarity search - Function
Uracil-DNA glycosylase family 4 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesSulfolobus tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsKawai, A. / Miyamoto, S.
CitationJournal: Febs Lett. / Year: 2015
Title: Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding
Authors: Kawai, A. / Higuchi, S. / Tsunoda, M. / Nakamura, K.T. / Yamagata, Y. / Miyamoto, S.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9994
Polymers22,3601
Non-polymers6393
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-22 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.030, 52.345, 74.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uracil-DNA glycosylase /


Mass: 22360.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: 7 / Gene: STK_22380 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96YD0, uracil-DNA glycosylase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 20% PEG3350, 0.1 M MES pH5.8, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 16590 / % possible obs: 99.7 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 25.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5.2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ZBX

4zbx


Resolution: 1.9→26.172 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 814 4.91 %
Rwork0.1603 --
obs0.1626 16566 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→26.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 26 154 1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091751
X-RAY DIFFRACTIONf_angle_d1.1262383
X-RAY DIFFRACTIONf_dihedral_angle_d13.758705
X-RAY DIFFRACTIONf_chiral_restr0.05251
X-RAY DIFFRACTIONf_plane_restr0.006308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.01910.24491380.17112551X-RAY DIFFRACTION99
2.0191-2.17490.22051330.15172589X-RAY DIFFRACTION100
2.1749-2.39360.20381330.14922603X-RAY DIFFRACTION100
2.3936-2.73970.22341340.162619X-RAY DIFFRACTION100
2.7397-3.45050.21711330.15452647X-RAY DIFFRACTION100
3.4505-26.1750.18191430.16782743X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -24.7866 Å / Origin y: 0.4195 Å / Origin z: 8.7126 Å
111213212223313233
T0.1322 Å2-0.0114 Å2-0.0149 Å2-0.1023 Å2-0.0008 Å2--0.1288 Å2
L1.77 °2-0.4329 °2-0.5408 °2-2.2301 °20.2711 °2--2.4103 °2
S-0.1037 Å °-0.0649 Å °-0.1412 Å °0.0043 Å °0.1812 Å °-0.0356 Å °0.2155 Å °0.0107 Å °-0.0631 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 192)

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