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- PDB-6k5g: Structural and catalytic analysis of two diverse uridine phosphor... -

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Basic information

Entry
Database: PDB / ID: 6k5g
TitleStructural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Phytophthora capsici / uridine phosphorylases / Uridine
Function / homologyuridine phosphorylase / nucleoside metabolic process / uridine phosphorylase activity / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Uridine phosphorylase
Function and homology information
Biological speciesPhytophthora capsici LT1534 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.574 Å
AuthorsYang, C.C. / Zhang, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaCARS-25-03B China
CitationJournal: Sci Rep / Year: 2020
Title: Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici.
Authors: Yang, C. / Li, J. / Huang, Z. / Zhang, X. / Gao, X. / Zhu, C. / Morris, P.F. / Zhang, X.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,15810
Polymers132,6064
Non-polymers5536
Water23,0591280
1
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5795
Polymers66,3032
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-22 kcal/mol
Surface area21980 Å2
MethodPISA
2
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5795
Polymers66,3032
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-24 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.246, 153.058, 67.280
Angle α, β, γ (deg.)90.000, 115.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uridine phosphorylase


Mass: 33151.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora capsici LT1534 (eukaryote)
Strain: LT1534 / Gene: up / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A410UCT3, uridine phosphorylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1280 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1 MES monohydrate PH 6.0, 22% PEG 400 / PH range: 5.6-6.4

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 144078 / % possible obs: 98.9 % / Redundancy: 3.4 % / Net I/σ(I): 6.6
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 5837 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
BLU-MAXdata collection
PDB_EXTRACTdata extraction
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.574→47.509 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.2172 7284 5.06 %
Rwork0.1862 --
obs0.1877 144078 85.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.87 Å2 / Biso mean: 18.7019 Å2 / Biso min: 3.9 Å2
Refinement stepCycle: final / Resolution: 1.574→47.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8814 0 84 1280 10178
Biso mean--15.34 28.7 -
Num. residues----1179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5736-1.59150.3975710.30831353142425
1.5915-1.61030.2723890.29821907199636
1.6103-1.62990.27251420.26952275241743
1.6299-1.65050.30851510.2682682283351
1.6505-1.67220.31681650.2523207337259
1.6722-1.69520.25621720.24593491366366
1.6952-1.71940.28042160.24673983419974
1.7194-1.7450.26962200.23324358457882
1.745-1.77230.28242390.22984662490186
1.7723-1.80140.25962490.22664754500390
1.8014-1.83240.23263010.21025022532394
1.8324-1.86570.21532860.20285156544296
1.8657-1.90160.22822800.2045192547298
1.9016-1.94050.22772960.20195152544897
1.9405-1.98260.25763000.19355243554398
1.9826-2.02880.21332870.18595176546398
2.0288-2.07950.23963010.17835217551898
2.0795-2.13570.20632900.17745249553998
2.1357-2.19860.22072700.17945214548498
2.1986-2.26950.19042520.17725274552698
2.2695-2.35060.20732700.17515272554298
2.3506-2.44480.23352830.17755290557399
2.4448-2.5560.21822700.17815281555199
2.556-2.69080.21212670.17065309557698
2.6908-2.85930.2032970.17795126542397
2.8593-3.08010.20452830.17585290557398
3.0801-3.38990.19232740.1745238551298
3.3899-3.88030.18952280.16695196542496
3.8803-4.8880.17032580.16475090534894
4.888-47.53070.2422770.20035135541295

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