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- PDB-5h0k: The crystal structure of WT Pedobacter heparinus SMUG2 -

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Basic information

Entry
Database: PDB / ID: 5h0k
TitleThe crystal structure of WT Pedobacter heparinus SMUG2
ComponentsUncharacterized protein
KeywordsLYASE / SMUG / DNA damage / glycosylase
Function / homologyDNA glycosylase Phe SMUG2-like / : / Uracil-DNA glycosylase-like domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesPedobacter heparinus DSM 2366 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsXie, W. / Cao, W. / Pang, P.
Funding support China, 4items
OrganizationGrant numberCountry
Fundamental Research Funds for the Central Universities16lgjc76 China
the Science and Technology Program of Guangzhou201504010025 China
Foundation of Key Laboratory of Gene Engineering of the Ministry of Education201502 China
Guangdong Innovative Research Team ProgramNO. 2011Y038 China
CitationJournal: Biochem. J. / Year: 2017
Title: SMUG2 DNA glycosylase from Pedobacter heparinus as a new subfamily of the UDG superfamily
Authors: Pang, P. / Yang, Y. / Li, J. / Wang, Z. / Cao, W. / Xie, W.
History
DepositionOct 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,3151
Polymers28,3151
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10930 Å2
Unit cell
Length a, b, c (Å)56.714, 56.714, 144.539
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-357-

HOH

21A-445-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 28314.516 Da / Num. of mol.: 1 / Mutation: G65Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus DSM 2366 (bacteria)
Strain: DSM 2366 / Production host: Escherichia coli (E. coli) / References: UniProt: C6Y1J8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 27% PEG 3350,0.25 M NaCl, 0.1M Tris-HCl pH 8.5/0.1M Hepes pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 12005 / % possible obs: 99.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 19.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 8.5 / CC1/2: 0.946 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→38.643 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.52
RfactorNum. reflection% reflection
Rfree0.2464 622 5.21 %
Rwork0.201 --
obs0.2033 11928 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→38.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 147 2047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061952
X-RAY DIFFRACTIONf_angle_d0.9462634
X-RAY DIFFRACTIONf_dihedral_angle_d12.4361159
X-RAY DIFFRACTIONf_chiral_restr0.058276
X-RAY DIFFRACTIONf_plane_restr0.008336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2438-2.46960.30951550.23652729X-RAY DIFFRACTION99
2.4696-2.82690.29611490.21682773X-RAY DIFFRACTION100
2.8269-3.56120.24371560.19912813X-RAY DIFFRACTION100
3.5612-38.64880.20661620.1842991X-RAY DIFFRACTION100

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