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- PDB-5x3g: The WT UNG crystal structure from Nitratifractor salsuginis -

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Basic information

Entry
Database: PDB / ID: 5x3g
TitleThe WT UNG crystal structure from Nitratifractor salsuginis
ComponentsUracil-DNA glycosylase
KeywordsDNA BINDING PROTEIN / uracil DNA glycosylase / base excision repair / single-wavelength anomalous dispersion
Function / homologybase-excision repair, AP site formation via deaminated base removal / Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase-like domain superfamily / uracil DNA N-glycosylase activity / Uracil-DNA glycosylase
Function and homology information
Biological speciesNitratifractor salsuginis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.021 Å
AuthorsXie, W. / Cao, W. / Chen, R. / Zhang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Fundamental Research Funds for the Central Universities16lgjc76 China
the Science and Technology Program of Guangzhou201504010025 China
CitationJournal: FEBS J. / Year: 2017
Title: An unconventional family 1 uracil DNA glycosylase in Nitratifractor salsuginis.
Authors: Li, J. / Chen, R. / Yang, Y. / Zhang, Z. / Fang, G.C. / Xie, W. / Cao, W.
History
DepositionFeb 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)30,8331
Polymers30,8331
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11470 Å2
Unit cell
Length a, b, c (Å)37.874, 59.393, 99.678
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: 30833.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratifractor salsuginis (bacteria) / Strain: DSM 16511 / JCM 12458 / E9I37-1 / Gene: Nitsa_0175 / Production host: Escherichia coli (E. coli) / References: UniProt: E6WYZ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 32.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% PEG3350, 0.1 M HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CCD / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 15396 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 25.3
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 13 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 3 / Num. unique obs: 1517 / CC1/2: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.021→31.934 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.54
RfactorNum. reflection% reflection
Rfree0.2608 748 4.9 %
Rwork0.2132 --
obs0.2155 15253 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.021→31.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 0 105 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032013
X-RAY DIFFRACTIONf_angle_d0.6462733
X-RAY DIFFRACTIONf_dihedral_angle_d15.9381217
X-RAY DIFFRACTIONf_chiral_restr0.041303
X-RAY DIFFRACTIONf_plane_restr0.004356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.021-2.1770.3341610.23632832X-RAY DIFFRACTION100
2.177-2.39610.34181390.30692804X-RAY DIFFRACTION97
2.3961-2.74260.33111330.23252906X-RAY DIFFRACTION100
2.7426-3.45480.24091600.22132915X-RAY DIFFRACTION100
3.4548-31.93770.22471550.17923048X-RAY DIFFRACTION100

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