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- PDB-5oln: X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 5oln
TitleX-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis at 1.88 A
ComponentsPyrimidine-nucleoside phosphorylase
KeywordsTRANSFERASE / Pyrimidine-nucleoside phosphorylase / NP-2 superfamily
Function / homology
Function and homology information


deoxyuridine phosphorylase activity / pyrimidine-nucleoside phosphorylase / pyrimidine nucleoside metabolic process / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / uridine phosphorylase activity / metal ion binding / cytosol
Similarity search - Function
Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C ...Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Pyrimidine-nucleoside phosphorylase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsBalaev, V.V. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Betzel, C. / Lashkov, A.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Grant of the President of Russian FederationMK-9246.2016.3. Russian Federation
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of pyrimidine-nucleoside phosphorylase from Bacillus subtilis in complex with imidazole and sulfate.
Authors: Balaev, V.V. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Betzel, C. / Lashkov, A.A.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Pyrimidine-nucleoside phosphorylase
B: Pyrimidine-nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0327
Polymers92,6662
Non-polymers3655
Water8,107450
1
A: Pyrimidine-nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4643
Polymers46,3331
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyrimidine-nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5674
Polymers46,3331
Non-polymers2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.368, 93.010, 139.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyrimidine-nucleoside phosphorylase / Py-NPase


Mass: 46333.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pdp, BSU39400 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P39142, pyrimidine-nucleoside phosphorylase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M Amonium acetate, 0.1 M Bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.88→77.447 Å / Num. all: 67839 / Num. obs: 67839 / % possible obs: 98.4 % / Redundancy: 11.1 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.207 / Rsym value: 0.198 / Net I/av σ(I): 3.1 / Net I/σ(I): 8.5 / Num. measured all: 755376
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.88-1.9811.61.0550.711293397250.321.1031.0552.497.7
1.98-2.111.30.7141.110399091950.220.7480.7143.498
2.1-2.2511.10.4921.69580985990.1520.5160.4924.697
2.25-2.4311.60.3682.19436681330.1120.3850.368698.4
2.43-2.66110.2772.78316875340.0870.2910.2777.198.5
2.66-2.9711.30.2013.67724468470.0620.2110.2019.698.7
2.97-3.43110.1494.56680661010.0470.1560.1491399.2
3.43-4.210.60.1115.35524152170.0360.1170.1111999.4
4.2-5.9510.40.0955.84265341090.0310.10.09520.799.6
5.95-46.6189.70.0676.42316623790.0220.070.06721.999.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.74 Å46.5 Å
Translation7.74 Å46.5 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
SCALA3.3.22data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EP8

5ep8


Resolution: 1.88→46.505 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 3363 4.96 %RANDOM
Rwork0.1995 ---
obs0.2014 67757 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.36 Å2 / Biso mean: 30.1925 Å2 / Biso min: 10.56 Å2
Refinement stepCycle: final / Resolution: 1.88→46.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 28 450 6951
Biso mean--34.16 29.76 -
Num. residues----867

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