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- PDB-7q32: Mutant D24G of uridine phosphorylase from E. coli -

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Basic information

Entry
Database: PDB / ID: 7q32
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
CITRATE ANION / : / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSafonova, T. / Polyakov, K. / Antipov, A. / Okorokova, N. / Mordkovich, N. / Veiko, V.
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. / Antipov, A. / Okorokova, N. / Mordkovich, N. / Veiko, V.
History
DepositionOct 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jan 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)53,9845
Polymers53,5672
Non-polymers4173
Water5,981332
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)161,95315
Polymers160,7016
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 area22950 Å2
ΔGint-113 kcal/mol
Surface area47310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.070, 150.070, 46.360
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-558-

HOH

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Components

#1: Protein Uridine phosphorylase / UPase / UrdPase


Mass: 26783.564 Da / Num. of mol.: 2 / Mutation: D27G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: udp, b3831, JW3808 / Production host: Escherichia coli (E. coli) / References: UniProt: P12758, uridine phosphorylase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 34.42 %
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: 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: 1.68→30 Å / Num. obs: 44388 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 1 / Net I/σ(I): 9.9
Reflection shellResolution: 1.68→1.72 Å / Num. unique obs: 3315 / CC1/2: 0.58

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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: 1.7→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.567 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2021 2155 5.027 %
Rwork0.154 40717 -
all0.156 --
obs-42872 99.967 %
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: 28.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.124 Å2-0.062 Å20 Å2
2---0.124 Å20 Å2
3---0.403 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 27 332 4111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123899
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.6365297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3321.848184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56615657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2761526
X-RAY DIFFRACTIONr_chiral_restr0.1370.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022936
X-RAY DIFFRACTIONr_nbd_refined0.2170.21903
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2309
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.233
X-RAY DIFFRACTIONr_mcbond_it2.3522.5751998
X-RAY DIFFRACTIONr_mcangle_it2.8763.8462494
X-RAY DIFFRACTIONr_scbond_it4.292.941901
X-RAY DIFFRACTIONr_scangle_it5.7074.2462803
X-RAY DIFFRACTIONr_lrange_it5.94637.5116119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.2971990.2882981X-RAY DIFFRACTION99.9686
1.744-1.7920.2861640.2472910X-RAY DIFFRACTION100
1.792-1.8440.31430.2272892X-RAY DIFFRACTION100
1.844-1.9010.2761520.1972743X-RAY DIFFRACTION100
1.901-1.9630.2131310.1622711X-RAY DIFFRACTION99.9648
1.963-2.0320.2361320.172598X-RAY DIFFRACTION100
2.032-2.1080.2081320.1672507X-RAY DIFFRACTION99.9621
2.108-2.1940.2051400.162395X-RAY DIFFRACTION99.9212
2.194-2.2920.1991060.1452317X-RAY DIFFRACTION99.9587
2.292-2.4040.2081390.1462193X-RAY DIFFRACTION100
2.404-2.5330.1871130.1332105X-RAY DIFFRACTION100
2.533-2.6870.197960.1371993X-RAY DIFFRACTION100
2.687-2.8720.181720.1351908X-RAY DIFFRACTION99.8991
2.872-3.1020.209780.1551745X-RAY DIFFRACTION99.8904
3.102-3.3970.212870.1361602X-RAY DIFFRACTION100
3.397-3.7970.15760.1211439X-RAY DIFFRACTION100
3.797-4.3830.129740.1151267X-RAY DIFFRACTION99.9255
4.383-5.3630.179370.1341100X-RAY DIFFRACTION100
5.363-7.5660.17480.16833X-RAY DIFFRACTION100
7.566-100.208340.175450X-RAY DIFFRACTION99.5885

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