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- PDB-7q1i: Hybrid form of uridine phosphorylase from E. coli and Salmonella ... -

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Basic information

Entry
Database: PDB / ID: 7q1i
TitleHybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence glycerol
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / hybrid enzyme
Function / homology
Function and homology information


nucleoside catabolic process / uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine phosphorylase activity / cytoplasm
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
CITRATE ANION / : / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli MS 85-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPolyakov, K. / Safonova, T.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Not funded Russian Federation
CitationJournal: To Be Published
Title: Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence glycerol
Authors: Polyakov, K. / Safonova, T.
History
DepositionOct 20, 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)54,5519
Polymers53,7652
Non-polymers7867
Water5,603311
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)163,65327
Polymers161,2966
Non-polymers2,35721
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 area25990 Å2
ΔGint-111 kcal/mol
Surface area47310 Å2
Unit cell
Length a, b, c (Å)150.520, 150.520, 46.250
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-562-

HOH

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Components

#1: Protein Uridine phosphorylase


Mass: 26882.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli MS 85-1 (bacteria) / Gene: udp, HMPREF9350_04039 / Production host: Escherichia coli (E. coli) / References: UniProt: E6BNQ3, 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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 1.88 Å3/Da / Density % sol: 34.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium citrate tribasic monohydrate, 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: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.8025 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8025 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 50485 / % possible obs: 97.9 % / Redundancy: 2.24 % / CC1/2: 1 / Net I/σ(I): 7.9
Reflection shellResolution: 1.65→1.69 Å / Num. unique obs: 3253 / CC1/2: 0.6

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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: 1.65→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.251 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.118
RfactorNum. reflection% reflection
Rfree0.2293 2353 5.058 %
Rwork0.1788 44170 -
all0.181 --
obs-46523 98.947 %
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: 19.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.237 Å20.118 Å2-0 Å2
2--0.237 Å2-0 Å2
3----0.768 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 51 311 4128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0123900
X-RAY DIFFRACTIONr_angle_refined_deg2.3521.6375293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81121.848184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6315651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7821527
X-RAY DIFFRACTIONr_chiral_restr0.1470.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022934
X-RAY DIFFRACTIONr_nbd_refined0.2220.21881
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22685
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2286
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.228
X-RAY DIFFRACTIONr_mcbond_it2.1651.772003
X-RAY DIFFRACTIONr_mcangle_it2.6042.6412500
X-RAY DIFFRACTIONr_scbond_it3.3042.0191897
X-RAY DIFFRACTIONr_scangle_it4.412.9152791
X-RAY DIFFRACTIONr_lrange_it4.77125.4456026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.2721700.263297X-RAY DIFFRACTION99.1138
1.693-1.7390.2811620.2563165X-RAY DIFFRACTION99.2838
1.739-1.790.2771360.2343146X-RAY DIFFRACTION99.3642
1.79-1.8450.2911760.2273046X-RAY DIFFRACTION99.4751
1.845-1.9050.2631320.2022931X-RAY DIFFRACTION99.1583
1.905-1.9720.2761490.2072816X-RAY DIFFRACTION99.2635
1.972-2.0460.2511480.22746X-RAY DIFFRACTION99.416
2.046-2.130.241450.2012621X-RAY DIFFRACTION99.3178
2.13-2.2240.271690.2012465X-RAY DIFFRACTION99.0598
2.224-2.3330.2241030.1882407X-RAY DIFFRACTION98.8189
2.333-2.4590.241390.1882280X-RAY DIFFRACTION98.8557
2.459-2.6080.2721070.1872166X-RAY DIFFRACTION99.1278
2.608-2.7880.2171220.1891995X-RAY DIFFRACTION98.6487
2.788-3.0110.279910.1811898X-RAY DIFFRACTION98.5629
3.011-3.2980.2151150.1581723X-RAY DIFFRACTION98.4995
3.298-3.6860.19850.1421538X-RAY DIFFRACTION97.3605
3.686-4.2540.146890.1231351X-RAY DIFFRACTION97.7597
4.254-5.2060.186660.1241156X-RAY DIFFRACTION98.469
5.206-7.3460.19340.156913X-RAY DIFFRACTION98.6458
7.346-100.188150.138503X-RAY DIFFRACTION96.2825

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