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- PDB-6k5k: Structural and catalytic analysis of two diverse uridine phosphor... -

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Basic information

Entry
Database: PDB / ID: 6k5k
TitleStructural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylases / phytophthora capsici / DUR
Function / homologyuridine phosphorylase / nucleoside metabolic process / uridine phosphorylase activity / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / 2'-DEOXYURIDINE / PHOSPHATE ION / Uridine phosphorylase
Function and homology information
Biological speciesPhytophthora capsici LT1534 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.097 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 29, 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)133,89912
Polymers132,6064
Non-polymers1,2938
Water9,602533
1
A: Uridine phosphorylase
C: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9496
Polymers66,3032
Non-polymers6464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-27 kcal/mol
Surface area21050 Å2
MethodPISA
2
B: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9496
Polymers66,3032
Non-polymers6464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-25 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.790, 97.382, 188.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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 (E. coli) / References: UniProt: A0A410UCT3, uridine phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DUR / 2'-DEOXYURIDINE


Mass: 228.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M sodium citrate tribasic dihydrate PH 5.0, 22% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 72543 / % possible obs: 99.9 % / Redundancy: 13.9 % / Net I/σ(I): 16.9
Reflection shellResolution: 2.09→2.14 Å / Num. unique obs: 7120

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.097→48.691 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.01
RfactorNum. reflection% reflection
Rfree0.317 3655 5.04 %
Rwork0.2462 --
obs0.2497 72543 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.09 Å2 / Biso mean: 33.0255 Å2 / Biso min: 7.83 Å2
Refinement stepCycle: final / Resolution: 2.097→48.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8606 0 129 533 9268
Biso mean--26.77 32.23 -
Num. residues----1151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0969-2.12450.30921440.26422566271098
2.1245-2.15360.29831440.250726232767100
2.1536-2.18430.33271590.248925842743100
2.1843-2.2170.34231610.254326182779100
2.217-2.25160.29021400.248825982738100
2.2516-2.28850.28811240.24526472771100
2.2885-2.3280.37441390.253326372776100
2.328-2.37030.35011600.248526082768100
2.3703-2.41590.33821380.248126352773100
2.4159-2.46520.29811370.251826222759100
2.4652-2.51880.33981110.25426772788100
2.5188-2.57740.35241190.243426602779100
2.5774-2.64180.32821310.231326342765100
2.6418-2.71330.32821610.245326132774100
2.7133-2.79310.33821500.247626592809100
2.7931-2.88320.31051370.236326602797100
2.8832-2.98630.32091510.252726022753100
2.9863-3.10580.34581320.252526702802100
3.1058-3.24710.28811360.25232660279699
3.2471-3.41830.31711460.243126442790100
3.4183-3.63240.31061620.23662643280599
3.6324-3.91270.29561420.227827072849100
3.9127-4.30630.27951320.22582671280399
4.3063-4.92890.29821410.21832700284199
4.9289-6.20790.32211300.26152753288399
6.2079-48.70410.35111280.29572797292596

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