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- PDB-5grk: Crystal structure of Uracil DNA glycosylase -Xanthine complex fro... -

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Basic information

Entry
Database: PDB / ID: 5grk
TitleCrystal structure of Uracil DNA glycosylase -Xanthine complex from Bradyrhizobium diazoefficiens
ComponentsBlr0248 protein
KeywordsHYDROLASE / Uracil DNA glycosylase (UDG) Bradyrhizobium diazoefficiens / nitrogen fixing symbiont / DNA repair / Xanthine.
Function / homologyUracil-DNA glycosylase-like domain superfamily / XANTHINE / Blr0248 protein
Function and homology information
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.804 Å
AuthorsPatil, V.V. / Ullas, V.C. / Ahn, W. / 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
DepositionAug 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5128
Polymers118,9034
Non-polymers6084
Water00
1
A: Blr0248 protein
B: Blr0248 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7564
Polymers59,4522
Non-polymers3042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-18 kcal/mol
Surface area22760 Å2
MethodPISA
2
C: Blr0248 protein
D: Blr0248 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7564
Polymers59,4522
Non-polymers3042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-19 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.023, 89.894, 255.339
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 / UDG / 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) / References: UniProt: Q89XR0
#2: Chemical
ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N4O2
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: 3.38 Å3/Da / Density % sol: 63.6 %
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: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.804→47.174 Å / Num. obs: 40422 / % possible obs: 99.91 % / Redundancy: 13.2 % / Net I/σ(I): 15.13
Reflection shellResolution: 2.8→2.85 Å

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementResolution: 2.804→47.174 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 1996 4.95 %
Rwork0.2201 --
obs0.2214 40340 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.804→47.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 44 0 8440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048685
X-RAY DIFFRACTIONf_angle_d0.81911846
X-RAY DIFFRACTIONf_dihedral_angle_d11.3263096
X-RAY DIFFRACTIONf_chiral_restr0.0321269
X-RAY DIFFRACTIONf_plane_restr0.0041532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8042-2.87430.40691390.29472672X-RAY DIFFRACTION100
2.8743-2.9520.30131400.29292677X-RAY DIFFRACTION100
2.952-3.03880.3651410.28162725X-RAY DIFFRACTION100
3.0388-3.13690.28891390.27592685X-RAY DIFFRACTION100
3.1369-3.2490.28961420.27512712X-RAY DIFFRACTION100
3.249-3.3790.31381420.25972714X-RAY DIFFRACTION100
3.379-3.53280.28031410.2512716X-RAY DIFFRACTION100
3.5328-3.7190.24581430.22272736X-RAY DIFFRACTION100
3.719-3.95190.24961430.2152737X-RAY DIFFRACTION100
3.9519-4.25680.17031410.17982729X-RAY DIFFRACTION100
4.2568-4.68480.19521440.16732766X-RAY DIFFRACTION100
4.6848-5.36190.19951440.17262780X-RAY DIFFRACTION100
5.3619-6.75230.20861450.19872796X-RAY DIFFRACTION100
6.7523-47.1810.20891520.20332899X-RAY DIFFRACTION98

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