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- PDB-7eyl: Crystal structure of Salmonella enterica ppnP -

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Basic information

Entry
Database: PDB / ID: 7eyl
TitleCrystal structure of Salmonella enterica ppnP
ComponentsPyrimidine/purine nucleoside phosphorylase
KeywordsHYDROLASE / Pyrimidine / purine / nucleoside phosphorylase
Function / homology
Function and homology information


pyrimidine-nucleoside phosphorylase / thymidine phosphorylase activity / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Pyrimidine/purine nucleoside phosphorylase / Pyrimidine/purine nucleoside phosphorylase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Pyrimidine/purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWen, Y. / Wu, B.X.
CitationJournal: Proteins / Year: 2022
Title: Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase revealed a Cupin fold.
Authors: Wen, Y. / Li, X. / Guo, W. / Wu, B.
History
DepositionMay 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrimidine/purine nucleoside phosphorylase
B: Pyrimidine/purine nucleoside phosphorylase


Theoretical massNumber of molelcules
Total (without water)20,5072
Polymers20,5072
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-15 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.571, 34.571, 124.885
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Pyrimidine/purine nucleoside phosphorylase / Adenosine phosphorylase / Cytidine phosphorylase / Guanosine phosphorylase / Inosine phosphorylase ...Adenosine phosphorylase / Cytidine phosphorylase / Guanosine phosphorylase / Inosine phosphorylase / Thymidine phosphorylase / Uridine phosphorylase / Xanthosine phosphorylase


Mass: 10253.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: ppnP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W4AVI3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 51977 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.037 / Rrim(I) all: 0.079 / Net I/σ(I): 7.824
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 7.824 / Num. unique obs: 5098 / CC1/2: 0.946 / CC star: 0.986 / Rpim(I) all: 0.11 / Rrim(I) all: 0.227 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EYJ

7eyj


Resolution: 1.2→20 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 2611 5.07 %
Rwork0.1738 --
obs0.1746 51507 99 %
Displacement parametersBiso mean: 17.69 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 200 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441484
X-RAY DIFFRACTIONf_angle_d0.84062015
X-RAY DIFFRACTIONf_chiral_restr0.0829224
X-RAY DIFFRACTIONf_plane_restr0.0057258
X-RAY DIFFRACTIONf_dihedral_angle_d16.3242863

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