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- PDB-4yjk: Crystal structure of C212S mutant of Shewanella oneidensis MR-1 u... -

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Basic information

Entry
Database: PDB / ID: 4yjk
TitleCrystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uracil / S212C mutant / uridine phosphorylase
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URACIL / Uridine phosphorylase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSafonova, T.N. / Mordkovich, N.N. / Manuvera, V.A. / Dorovatovsky, P.V. / Veiko, V.P. / Popov, V.O. / Polyakov, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Concerted action of two subunits of the functional dimer of Shewanella oneidensis MR-1 uridine phosphorylase derived from a comparison of the C212S mutant and the wild-type enzyme.
Authors: Safonova, T.N. / Mordkovich, N.N. / Veiko, V.P. / Okorokova, N.A. / Manuvera, V.A. / Dorovatovskii, P.V. / Popov, V.O. / Polyakov, K.M.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Jan 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
D: Uridine phosphorylase
F: Uridine phosphorylase
A: Uridine phosphorylase
C: Uridine phosphorylase
E: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,37118
Polymers161,1706
Non-polymers1,20112
Water15,151841
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24170 Å2
ΔGint-275 kcal/mol
Surface area42320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.230, 95.400, 91.200
Angle α, β, γ (deg.)90.00, 119.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uridine phosphorylase /


Mass: 26861.615 Da / Num. of mol.: 6 / Mutation: C212S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: udp, SO_4133 / Plasmid: pC212S / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q8E9X9, uridine phosphorylase
#2: Chemical ChemComp-URA / URACIL / Uracil


Mass: 112.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.982 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.471
11H+L, -K, -L20.064
11L, -K, H30.056
11L, K, -H-L40.06
11-H-L, K, H50.182
11-H, -K, H+L60.166
ReflectionResolution: 1.68→19.35 Å / Num. all: 151200 / Num. obs: 151200 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.7 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2X

4r2x


Resolution: 1.68→19.35 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.323 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16142 7639 5.1 %RANDOM
Rwork0.13797 ---
obs0.13918 143534 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.952 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å2-0 Å2-1.42 Å2
2--14.48 Å20 Å2
3----12.05 Å2
Refinement stepCycle: LAST / Resolution: 1.68→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10886 0 69 841 11796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911180
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210619
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.95115221
X-RAY DIFFRACTIONr_angle_other_deg1.032324330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90151457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71223.591440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.306151729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0851575
X-RAY DIFFRACTIONr_chiral_restr0.1160.21813
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022476
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1971.4075864
X-RAY DIFFRACTIONr_mcbond_other1.1971.4075863
X-RAY DIFFRACTIONr_mcangle_it1.7622.1047309
X-RAY DIFFRACTIONr_mcangle_other1.7622.1057310
X-RAY DIFFRACTIONr_scbond_it1.371.5315316
X-RAY DIFFRACTIONr_scbond_other1.3681.5315312
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0292.2467906
X-RAY DIFFRACTIONr_long_range_B_refined3.35711.64213203
X-RAY DIFFRACTIONr_long_range_B_other3.24511.47512866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 510 -
Rwork0.205 9442 -
obs--87.62 %

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