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- PDB-7eym: Crystal structure of Vibrio cholerae ppnP -

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Basic information

Entry
Database: PDB / ID: 7eym
TitleCrystal structure of Vibrio cholerae 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 speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,5472
Polymers20,5472
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-16 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.242, 55.242, 111.851
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: 10273.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ppnP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6V0E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 30% w/v Polyethylene glycol 8,000

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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: 1.38→50 Å / Num. obs: 35454 / % possible obs: 99.6 % / Redundancy: 12.5 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 26.333
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.901 / Mean I/σ(I) obs: 1.667 / Num. unique obs: 6596 / CC1/2: 0.576 / CC star: 0.855 / Rpim(I) all: 0.364 / Rrim(I) all: 0.976 / % possible all: 97.1

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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: 1.38→20 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 1784 5.03 %
Rwork0.2054 --
obs0.2064 35447 97.43 %
Displacement parametersBiso mean: 17.44 Å2
Refinement stepCycle: LAST / Resolution: 1.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 0 110 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661526
X-RAY DIFFRACTIONf_angle_d0.85812082
X-RAY DIFFRACTIONf_chiral_restr0.0786237
X-RAY DIFFRACTIONf_plane_restr0.0051274
X-RAY DIFFRACTIONf_dihedral_angle_d19.5562890

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