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- PDB-5gn2: Crystal structure of Uracil DNA glycosylase (BdiUNG) from Bradyrh... -

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Basic information

Entry
Database: PDB / ID: 5gn2
TitleCrystal structure of Uracil DNA glycosylase (BdiUNG) from Bradyrhizobium diazoefficiens
ComponentsBlr0248 protein
KeywordsHYDROLASE / Uracil DNA glycosylase (UDG) / Bradyrhizobium diazoefficiens / nitrogen fixing symbion
Function / homologyUracil-DNA glycosylase-like domain superfamily / Blr0248 protein
Function and homology information
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.952 Å
AuthorsPatil, V.V. / Chembazhi, U.V. / Varshney, U. / Woo, E.
Citation
Journal: Nucleic Acids Res. / Year: 2017
Title: Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity
Authors: Chembazhi, U.V. / Patil, V.V. / Sah, S. / Reeve, W. / Tiwari, R.P. / Woo, E. / Varshney, U.
#1: Journal: NUCLEIC ACIDS RES. / Year: 2015
Title: A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily
Authors: Sang, P.B. / Srinath, T. / Patil, A.G. / Woo, E. / Varshney, U.
History
DepositionJul 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 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: Blr0248 protein
B: Blr0248 protein
C: Blr0248 protein
D: Blr0248 protein


Theoretical massNumber of molelcules
Total (without water)118,9034
Polymers118,9034
Non-polymers00
Water10,215567
1
A: Blr0248 protein
B: Blr0248 protein


Theoretical massNumber of molelcules
Total (without water)59,4522
Polymers59,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-27 kcal/mol
Surface area22980 Å2
MethodPISA
2
C: Blr0248 protein
D: Blr0248 protein


Theoretical massNumber of molelcules
Total (without water)59,4522
Polymers59,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.652, 90.031, 255.671
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
Blr0248 protein / Uracil DNA glycosylase


Mass: 29725.795 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Strain: USDA 110 / Gene: blr0248 / Production host: Escherichia coli (E. coli) / Strain (production host): CC102 / References: UniProt: Q89XR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 3.42 Å3/Da / Density % sol: 64.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG3350, 200 mM sodium citrate, 100 mM sodium citrate/citric acid

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.952→30.524 Å / Num. obs: 117654 / % possible obs: 98.71 % / Redundancy: 4 % / Net I/σ(I): 13.34

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementResolution: 1.952→30.524 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2898 1994 1.69 %
Rwork0.2455 --
obs0.2462 117654 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→30.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 0 567 8963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098634
X-RAY DIFFRACTIONf_angle_d1.25611769
X-RAY DIFFRACTIONf_dihedral_angle_d12.6823094
X-RAY DIFFRACTIONf_chiral_restr0.0551268
X-RAY DIFFRACTIONf_plane_restr0.0071525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9525-2.00130.43311360.40697959X-RAY DIFFRACTION96
2.0013-2.05540.43091420.36828214X-RAY DIFFRACTION100
2.0554-2.11580.35661410.36628234X-RAY DIFFRACTION100
2.1158-2.18410.3861430.33278263X-RAY DIFFRACTION100
2.1841-2.26220.37611420.31548276X-RAY DIFFRACTION100
2.2622-2.35270.37021430.29928295X-RAY DIFFRACTION100
2.3527-2.45970.35671420.29038247X-RAY DIFFRACTION100
2.4597-2.58930.35141430.29178292X-RAY DIFFRACTION100
2.5893-2.75150.35621430.28318297X-RAY DIFFRACTION100
2.7515-2.96380.31911450.27628327X-RAY DIFFRACTION100
2.9638-3.26170.30191440.26138325X-RAY DIFFRACTION99
3.2617-3.7330.27891440.22478358X-RAY DIFFRACTION99
3.733-4.70040.20721430.18418285X-RAY DIFFRACTION97
4.7004-30.52740.22921430.18548288X-RAY DIFFRACTION94

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