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- PDB-7q31: Mutant D24G of uridine phosphorylase from E. coli -

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Basic information

Entry
Database: PDB / ID: 7q31
TitleMutant D24G of uridine phosphorylase from E. coli
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / mutant enzyme
Function / homology
Function and homology information


UMP catabolic process / uridine catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
: / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSafonova, T. / Polyakov, K.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Not funded Russian Federation
CitationJournal: To Be Published
Title: Mutant D24G of uridine phosphorylase from E. coli
Authors: Polyakov, K. / Safonova, T.
History
DepositionOct 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Uridine phosphorylase
BBB: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0838
Polymers53,5672
Non-polymers5156
Water6,197344
1
AAA: Uridine phosphorylase
BBB: Uridine phosphorylase
hetero molecules

AAA: Uridine phosphorylase
BBB: Uridine phosphorylase
hetero molecules

AAA: Uridine phosphorylase
BBB: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,24824
Polymers160,7016
Non-polymers1,54618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area22010 Å2
ΔGint-286 kcal/mol
Surface area48540 Å2
Unit cell
Length a, b, c (Å)150.100, 150.100, 50.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11AAA-302-

SO4

21BBB-301-

SO4

31BBB-301-

SO4

41AAA-514-

HOH

51AAA-567-

HOH

61BBB-561-

HOH

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Components

#1: Protein Uridine phosphorylase / UPase / UrdPase


Mass: 26783.564 Da / Num. of mol.: 2 / Mutation: D24G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: udp, b3831, JW3808 / Production host: Escherichia coli (E. coli) / References: UniProt: P12758, uridine phosphorylase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium sulfate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 41245 / % possible obs: 97.2 % / Redundancy: 2.6 % / CC1/2: 0.89 / Net I/σ(I): 11.1
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 3140 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2X

4r2x


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.437 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2185 2187 5.303 %
Rwork0.163 39057 -
all0.166 --
obs-41244 97.216 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.153 Å2
Baniso -1Baniso -2Baniso -3
1--0.403 Å2-0.202 Å20 Å2
2---0.403 Å20 Å2
3---1.308 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 27 344 4123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123865
X-RAY DIFFRACTIONr_angle_refined_deg2.2261.6365250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52621.62179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36915646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.071527
X-RAY DIFFRACTIONr_chiral_restr0.1340.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022882
X-RAY DIFFRACTIONr_nbd_refined0.2220.21936
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2292
X-RAY DIFFRACTIONr_metal_ion_refined0.0520.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.245
X-RAY DIFFRACTIONr_mcbond_it3.0052.6741998
X-RAY DIFFRACTIONr_mcangle_it3.5243.9942494
X-RAY DIFFRACTIONr_scbond_it4.7443.0271867
X-RAY DIFFRACTIONr_scangle_it5.994.3722756
X-RAY DIFFRACTIONr_lrange_it6.21838.8666074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.311640.2462975X-RAY DIFFRACTION98.463
1.795-1.8450.2761430.2362797X-RAY DIFFRACTION96.9977
1.845-1.8980.2661670.2192715X-RAY DIFFRACTION97.6287
1.898-1.9560.2761530.2072712X-RAY DIFFRACTION98.9637
1.956-2.0210.2691310.2012628X-RAY DIFFRACTION98.3951
2.021-2.0910.251260.1882527X-RAY DIFFRACTION98.405
2.091-2.170.2461200.1862467X-RAY DIFFRACTION98.6651
2.17-2.2590.2571310.1822333X-RAY DIFFRACTION97.7002
2.259-2.3590.251360.1782171X-RAY DIFFRACTION96.8514
2.359-2.4740.2021230.162147X-RAY DIFFRACTION97.6344
2.474-2.6080.2111490.1571997X-RAY DIFFRACTION97.6342
2.608-2.7660.2631000.1681902X-RAY DIFFRACTION97.2317
2.766-2.9570.2231050.1751767X-RAY DIFFRACTION95.559
2.957-3.1930.236820.1771619X-RAY DIFFRACTION94.3428
3.193-3.4970.247820.1681476X-RAY DIFFRACTION93.7989
3.497-3.9090.181750.1351356X-RAY DIFFRACTION94.3931
3.909-4.5120.159620.1131217X-RAY DIFFRACTION95.8052
4.512-5.5210.185700.1221012X-RAY DIFFRACTION95.7522
5.521-7.7860.181440.142794X-RAY DIFFRACTION96.7667
7.786-300.124240.128445X-RAY DIFFRACTION97.5052

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