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- PDB-7q1j: Hybrid form of uridine phosphorylase from E. coli and Salmonella ... -

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Basic information

Entry
Database: PDB / ID: 7q1j
TitleHybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence PEG
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / hybrid enzyme
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / 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: 1.71 Å
AuthorsSafonova, T. / Polyakov, K.
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 PEG
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)54,1835
Polymers53,7652
Non-polymers4173
Water5,098283
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)162,54815
Polymers161,2966
Non-polymers1,2529
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 area22100 Å2
ΔGint-118 kcal/mol
Surface area48230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.590, 150.590, 46.290
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
11BBB-536-

HOH

21BBB-540-

HOH

31BBB-546-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 34.53 %
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 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8025 Å / Relative weight: 1
ReflectionResolution: 1.71→30 Å / Num. obs: 42058 / % possible obs: 99.5 % / Redundancy: 3.82 % / CC1/2: 1 / Net I/σ(I): 9.6
Reflection shellResolution: 1.71→1.75 Å / Num. unique obs: 3091 / CC1/2: 0.7

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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: 1.71→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.261 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.157
RfactorNum. reflection% reflection
Rfree0.2808 2149 5.11 %
Rwork0.2037 39909 -
all0.208 --
obs-42058 99.451 %
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: 26.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.355 Å2-0 Å2
2--0.71 Å2-0 Å2
3----2.303 Å2
Refinement stepCycle: LAST / Resolution: 1.71→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 27 283 4076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0123864
X-RAY DIFFRACTIONr_angle_refined_deg2.6091.6375247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3155498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04621.758182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17415647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6741527
X-RAY DIFFRACTIONr_chiral_restr0.1770.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.022918
X-RAY DIFFRACTIONr_nbd_refined0.2320.21916
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2280
X-RAY DIFFRACTIONr_metal_ion_refined0.2340.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.229
X-RAY DIFFRACTIONr_mcbond_it3.8932.4911998
X-RAY DIFFRACTIONr_mcangle_it4.6673.7222494
X-RAY DIFFRACTIONr_scbond_it4.7522.8021866
X-RAY DIFFRACTIONr_scangle_it6.0294.0522753
X-RAY DIFFRACTIONr_lrange_it6.77335.5316025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.7540.3361610.3172928X-RAY DIFFRACTION99.5809
1.754-1.8020.3241570.2912887X-RAY DIFFRACTION99.4121
1.802-1.8550.3251640.2752768X-RAY DIFFRACTION99.4573
1.855-1.9120.3491440.2562728X-RAY DIFFRACTION99.446
1.912-1.9740.3381450.2622625X-RAY DIFFRACTION99.2831
1.974-2.0440.351570.2632516X-RAY DIFFRACTION99.1101
2.044-2.1210.3811230.2692449X-RAY DIFFRACTION98.9611
2.121-2.2070.3531490.2632375X-RAY DIFFRACTION99.2919
2.207-2.3050.3211160.2452268X-RAY DIFFRACTION99.1268
2.305-2.4180.3421070.2322165X-RAY DIFFRACTION99.3007
2.418-2.5480.294900.2122060X-RAY DIFFRACTION99.537
2.548-2.7030.2941050.2261979X-RAY DIFFRACTION99.7129
2.703-2.8890.356930.2181861X-RAY DIFFRACTION99.8467
2.889-3.120.303930.2091688X-RAY DIFFRACTION99.72
3.12-3.4170.245780.181602X-RAY DIFFRACTION99.8811
3.417-3.820.229700.1611411X-RAY DIFFRACTION99.6635
3.82-4.4090.174660.1191271X-RAY DIFFRACTION99.8506
4.409-5.3950.192660.1211058X-RAY DIFFRACTION99.8224
5.395-7.610.217430.142821X-RAY DIFFRACTION99.8844
7.61-100.137220.121449X-RAY DIFFRACTION98.7421

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