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- PDB-6k8p: Structural and catalytic analysis of two diverse uridine phosphor... -

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Basic information

Entry
Database: PDB / ID: 6k8p
TitleStructural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / phytophthora capsici / thymidine
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase / uridine phosphorylase activity / cytosol
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 1-O-phosphono-alpha-D-ribofuranose / THYMINE / THYMIDINE / Uridine phosphorylase
Similarity search - Component
Biological speciesPhytophthora capsici LT1534 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.965 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
DepositionJun 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 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.title / _citation.year
Revision 1.2Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)133,99312
Polymers132,6064
Non-polymers1,3878
Water10,521584
1
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9966
Polymers66,3032
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-29 kcal/mol
Surface area20910 Å2
MethodPISA
2
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9966
Polymers66,3032
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-29 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.956, 97.330, 188.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
Uridine phosphorylase


Mass: 33151.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: thymidine
Source: (gene. exp.) Phytophthora capsici LT1534 (eukaryote)
Gene: up / Production host: Escherichia coli (E. coli) / References: UniProt: A0A410UCT3, uridine phosphorylase
#4: Sugar ChemComp-R1P / 1-O-phosphono-alpha-D-ribofuranose / RIBOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-ribose / 1-O-phosphono-D-ribose / 1-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 590 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, potassium phosphate, magenesium chloride, cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 87357 / % possible obs: 99.7 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 11.9
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 8200

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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: MOLECULAR REPLACEMENT
Starting model: 6K5G

6k5g


Resolution: 1.965→38.463 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.6
RfactorNum. reflection% reflection
Rfree0.3156 4384 5.02 %
Rwork0.265 --
obs0.2675 87357 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.2 Å2 / Biso mean: 32.5664 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 1.965→38.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8596 0 146 584 9326
Biso mean--31.28 34.25 -
Num. residues----1148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.967-1.9870.37891230.3211230384
1.987-2.01040.30751300.2885273699
2.0104-2.03490.30671360.2745277299
2.0349-2.06070.31931570.27432699100
2.0607-2.08780.33991580.26522780100
2.0878-2.11640.30181390.26822784100
2.1164-2.14660.33781340.25442780100
2.1466-2.17870.28581340.25642755100
2.1787-2.21270.30771580.24932764100
2.2127-2.2490.29931460.24682739100
2.249-2.28780.25071400.2469275799
2.2878-2.32930.33131510.25752779100
2.3293-2.37410.31371360.25872790100
2.3741-2.42260.33151470.25162748100
2.4226-2.47530.32291380.25432809100
2.4753-2.53280.28971450.24932753100
2.5328-2.59620.3051170.23912810100
2.5962-2.66630.28221430.2425278199
2.6663-2.74480.31451300.2538279399
2.7448-2.83330.26931660.25462743100
2.8333-2.93460.32541770.25722794100
2.9346-3.0520.3021370.2636279699
3.052-3.19090.27411440.26122806100
3.1909-3.3590.3251380.2579279899
3.359-3.56930.32381710.2592275999
3.5693-3.84470.3061660.2602277598
3.8447-4.23110.29011450.2499282399
4.2311-4.84240.30551600.2452278898
4.8424-6.0970.33521510.2977286899
6.097-38.450.41271670.3433289196

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