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- PDB-6k5h: Structural and catalytic analysis of two diverse uridine phosphor... -

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Basic information

Entry
Database: PDB / ID: 6k5h
TitleStructural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylases / Phytophthora capsici / R1P
Function / homologyuridine phosphorylase / uridine phosphorylase activity / nucleoside metabolic process / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / 1-O-phosphono-alpha-D-ribofuranose / URACIL / Uridine phosphorylase
Function and homology information
Biological speciesPhytophthora capsici LT1534 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.503 Å
AuthorsYang, C.C. / Zhang, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China2017YFD0200600 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 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 2.1Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,97512
Polymers132,6064
Non-polymers1,3698
Water3,423190
1
A: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9876
Polymers66,3032
Non-polymers6844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-19 kcal/mol
Surface area21350 Å2
MethodPISA
2
B: Uridine phosphorylase
C: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9876
Polymers66,3032
Non-polymers6844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-16 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.975, 97.688, 188.865
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-URA / URACIL / Uracil


Mass: 112.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1 mes monohydrate pH 6.0, 22% PEG 400 / PH range: 5.6-6.2

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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: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 43174 / % possible obs: 100 % / Redundancy: 13.3 % / Net I/σ(I): 20.7
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 4118

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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: 2.503→48.844 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.76
RfactorNum. reflection% reflection
Rfree0.3488 2169 5.02 %
Rwork0.2561 --
obs0.2607 43174 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.65 Å2 / Biso mean: 43.1097 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: final / Resolution: 2.503→48.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8580 0 67 190 8837
Biso mean--33.44 35.14 -
Num. residues----1153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5028-2.5610.36121320.27372542267494
2.561-2.62510.38251180.261727222840100
2.6251-2.6960.36431600.260127042864100
2.696-2.77540.35341610.26426872848100
2.7754-2.86490.42831270.272727402867100
2.8649-2.96730.38821540.269827132867100
2.9673-3.08610.36811620.267427022864100
3.0861-3.22650.36731470.26827462893100
3.2265-3.39660.35071280.260527562884100
3.3966-3.60940.37271320.250327402872100
3.6094-3.88790.35681570.242927452902100
3.8879-4.2790.31271530.236127502903100
4.279-4.89770.2751450.21582784292999
4.8977-6.16860.34171490.26732802295199
6.1686-48.85330.37121440.28162872301696

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