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- PDB-5ep8: X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 5ep8
TitleX-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis with Sulfate Ion
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
Pyrimidine-nucleoside phosphorylase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å
AuthorsLashkov, A.A. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR14-04-00952 Russian Federation
CitationJournal: To Be Published
Title: X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis with Sulfate Ion
Authors: Lashkov, A.A. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Pyrimidine-nucleoside phosphorylase
B: Pyrimidine-nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8505
Polymers92,6342
Non-polymers2153
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-44 kcal/mol
Surface area34410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.463, 91.350, 109.800
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: 46317.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: pdp, BSU39400 / Plasmid: pET15b/pdp / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P39142, pyrimidine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Sodium acetate, PEG 3350

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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: Sep 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.66→70.224 Å / Num. all: 23783 / Num. obs: 23783 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.065 / Rsym value: 0.057 / Net I/av σ(I): 11.522 / Net I/σ(I): 17.7 / Num. measured all: 102504
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.66-2.84.40.8910.91508034240.4680.8911.799.7
2.8-2.974.30.4751.61384732390.2540.4752.999.3
2.97-3.184.50.2882.71377130420.150.288599.9
3.18-3.434.30.1664.71238228520.0880.1668.499.9
3.43-3.764.30.0858.91113526170.0460.08514.799.2
3.76-4.214.40.04615.61072924150.0240.04625.599.9
4.21-4.864.20.0323.3889821180.0160.0336.899
4.86-5.954.40.02624.8797518160.0140.02640.199.9
5.95-8.4140.02223.1565014300.0120.0224699.2
8.41-47.0563.70.01633.430378300.0090.01659.498

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.52
Highest resolutionLowest resolution
Rotation47.06 Å3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.21data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H5Q

3h5q


Resolution: 2.66→70.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2928 / WRfactor Rwork: 0.2154 / FOM work R set: 0.7122 / SU B: 21.081 / SU ML: 0.408 / SU Rfree: 0.4263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2928 1171 4.9 %RANDOM
Rwork0.2154 ---
obs0.2191 22573 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.01 Å2 / Biso mean: 75.353 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-7.45 Å2-0 Å20 Å2
2---4.34 Å2-0 Å2
3----3.11 Å2
Refinement stepCycle: final / Resolution: 2.66→70.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 11 27 6504
Biso mean--120.2 57.39 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196545
X-RAY DIFFRACTIONr_bond_other_d0.0020.026586
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.998832
X-RAY DIFFRACTIONr_angle_other_deg0.855315201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88825.952252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.651151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6291530
X-RAY DIFFRACTIONr_chiral_restr0.0610.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021245
X-RAY DIFFRACTIONr_mcbond_it2.7857.4023464
X-RAY DIFFRACTIONr_mcbond_other2.7837.4023463
X-RAY DIFFRACTIONr_mcangle_it4.56411.0984327
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 96 -
Rwork0.38 1635 -
all-1731 -
obs--99.65 %

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