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

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Basic information

Entry
Database: PDB / ID: 4zbx
TitleFamily 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=0.9000)
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 / : / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...: / Uracil-DNA glycosylase family 4 / : / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9073
Polymers22,3601
Non-polymers5472
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-22 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.189, 52.250, 74.453
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


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 46.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 20% PEG3350, 0.1M MES, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Sep 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 23097 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 50.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 6.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ui0

1ui0


Resolution: 1.7→36.925 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1166 5.06 %
Rwork0.169 --
obs0.1712 23045 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 20 150 1718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081717
X-RAY DIFFRACTIONf_angle_d1.0592335
X-RAY DIFFRACTIONf_dihedral_angle_d13.323689
X-RAY DIFFRACTIONf_chiral_restr0.046246
X-RAY DIFFRACTIONf_plane_restr0.006301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6997-1.77710.23991470.19052684X-RAY DIFFRACTION99
1.7771-1.87080.20411720.17742666X-RAY DIFFRACTION100
1.8708-1.9880.22861360.16482682X-RAY DIFFRACTION100
1.988-2.14150.21231360.16512704X-RAY DIFFRACTION100
2.1415-2.3570.20691380.16212735X-RAY DIFFRACTION100
2.357-2.69790.2371610.17772714X-RAY DIFFRACTION100
2.6979-3.39870.21541520.17622768X-RAY DIFFRACTION100
3.3987-36.93340.20481240.16262926X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.047 Å / Origin y: 0.297 Å / Origin z: 8.4553 Å
111213212223313233
T0.1604 Å2-0.0123 Å2-0.0093 Å2-0.1042 Å2-0.0001 Å2--0.1327 Å2
L2.087 °2-0.5861 °2-1.026 °2-2.2993 °20.4061 °2--2.8752 °2
S-0.1088 Å °-0.0493 Å °-0.1439 Å °-0.0083 Å °0.1781 Å °-0.0268 Å °0.2638 Å °0.011 Å °-0.088 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 192)

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