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- PDB-6kd3: Structural and catalytic analysis of two diverse uridine phosphor... -

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Basic information

Entry
Database: PDB / ID: 6kd3
TitleStructural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / phytophthora capsici
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesPhytophthora capsici LT1534 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.764 Å
AuthorsYang, C.C. / Zhang, X.G.
CitationJournal: To be published
Title: Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.
Authors: Yang, C.C. / Zhang, X.G.
History
DepositionJun 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)69,7142
Polymers69,7142
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-29 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.836, 66.386, 261.061
Angle α, β, γ (deg.)90.000, 96.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uridine phosphorylase


Mass: 34856.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora capsici LT1534 (eukaryote)
Strain: LT1534 / Production host: Escherichia coli (E. coli) / References: uridine phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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

Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium iodide, 20% PEG 3350

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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: Jun 3, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 31606 / % possible obs: 82 % / Redundancy: 4 % / Rmerge(I) obs: 0.235 / Net I/σ(I): 6.39
Reflection shellResolution: 2.76→2.86 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1242 / % possible all: 84.4

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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: MAD / Resolution: 2.764→47.45 Å / SU ML: 0.73 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 54.03
RfactorNum. reflection% reflection
Rfree0.4278 1585 5.01 %
Rwork0.3855 --
obs0.3877 31606 67.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.77 Å2 / Biso mean: 32.1619 Å2 / Biso min: 3.44 Å2
Refinement stepCycle: final / Resolution: 2.764→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 0 62 3894
Biso mean---25.94 -
Num. residues----588
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.768-2.85290.3386500.3121103826
2.8529-2.95480.3743950.35179145
2.9548-3.07310.41391210.376224957
3.0731-3.21290.43091490.3693270668
3.2129-3.38230.39931640.3627304076
3.3823-3.59410.42751750.358322581
3.5941-3.87150.42981600.3578323679
3.8715-4.26090.39521850.3697316479
4.2609-4.87690.42961420.3702313777
4.8769-6.14230.45061900.4153315778
6.1423-47.40.4711540.4599327878

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