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- PDB-7eyk: Crystal structure of Escherichia coli ppnP-Selenomethionine derived -

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Basic information

Entry
Database: PDB / ID: 7eyk
TitleCrystal structure of Escherichia coli ppnP-Selenomethionine derived
ComponentsPyrimidine/purine nucleoside phosphorylase
KeywordsHYDROLASE / Pyrimidine / purine / nucleoside phosphorylase
Function / homology
Function and homology information


pyrimidine-nucleoside phosphorylase activity / pyrimidine-nucleoside phosphorylase / thymidine phosphorylase activity / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / protein homodimerization activity / cytosol
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 speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrimidine/purine nucleoside phosphorylase


Theoretical massNumber of molelcules
Total (without water)10,4681
Polymers10,4681
Non-polymers00
Water2,720151
1
A: Pyrimidine/purine nucleoside phosphorylase

A: Pyrimidine/purine nucleoside phosphorylase


Theoretical massNumber of molelcules
Total (without water)20,9362
Polymers20,9362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area1990 Å2
ΔGint-18 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.658, 59.658, 52.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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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: 10468.095 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ppnP / Production host: Escherichia coli (E. coli) / References: UniProt: P0C037
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.26 M Ammonium sulfate (dibasic), 0.1M Sodium cacodylate/Hydrochloric acid pH 6.5

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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: 21812 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.96 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.018 / Rrim(I) all: 0.079 / Net I/σ(I): 36.41
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 7 / Num. unique obs: 2162 / CC1/2: 0.959 / CC star: 0.989 / Rpim(I) all: 0.116 / Rrim(I) all: 0.518

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→20 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1688 1062 4.87 %
Rwork0.1507 --
obs0.1515 21787 99.88 %
Displacement parametersBiso mean: 16.32 Å2
Refinement stepCycle: LAST / Resolution: 1.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 0 151 877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048773
X-RAY DIFFRACTIONf_angle_d0.87651056
X-RAY DIFFRACTIONf_chiral_restr0.09118
X-RAY DIFFRACTIONf_plane_restr0.0059138
X-RAY DIFFRACTIONf_dihedral_angle_d16.5515454

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