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- PDB-5x3h: The Y81G mutant of the UNG crystal structure from Nitratifractor ... -

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Basic information

Entry
Database: PDB / ID: 5x3h
TitleThe Y81G mutant of the UNG crystal structure from Nitratifractor salsuginis
ComponentsUracil-DNA glycosylase
KeywordsDNA BINDING PROTEIN / uracil DNA glycosylase / base excision repair
Function / homologybase-excision repair, AP site formation via deaminated base removal / Uracil-DNA glycosylase family 1 / uracil-DNA glycosylase / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXie, W. / Chen, R. / Cao, W. / 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 22, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)60,7982
Polymers60,7982
Non-polymers00
Water43224
1
A: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)30,3991
Polymers30,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)30,3991
Polymers30,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.414, 114.763, 55.536
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uracil-DNA glycosylase


Mass: 30398.912 Da / Num. of mol.: 2 / Mutation: Y81G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratifractor salsuginis (strain DSM 16511 / JCM 12458 / E9I37-1) (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.: 24 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
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: BL17U / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16628 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1623 / CC1/2: 0.92 / % possible all: 98.5

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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
Starting model: 5X3G

5x3g


Resolution: 2.5→39.9 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.41
RfactorNum. reflection% reflection
Rfree0.2654 737 4.47 %
Rwork0.2117 --
obs0.214 16470 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 0 24 3861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063925
X-RAY DIFFRACTIONf_angle_d1.0015336
X-RAY DIFFRACTIONf_dihedral_angle_d17.7022365
X-RAY DIFFRACTIONf_chiral_restr0.053601
X-RAY DIFFRACTIONf_plane_restr0.008695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.69090.38931330.26893043X-RAY DIFFRACTION95
2.6909-2.96170.31261360.27193221X-RAY DIFFRACTION100
2.9617-3.390.30821820.24423113X-RAY DIFFRACTION100
3.39-4.27030.26291550.19313201X-RAY DIFFRACTION99
4.2703-39.90.19651310.17833155X-RAY DIFFRACTION98

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