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- PDB-1y1q: Crystal Structure of the Uridine Phosphorylase from Salmonella Ty... -

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Basic information

Entry
Database: PDB / ID: 1y1q
TitleCrystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uridine-5p-monophosphate and Sulfate Ion at 2.35A Resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / 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
URIDINE-5'-MONOPHOSPHATE / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGabdoulkhakov, A.G. / Dontsova, M.V. / Kachalova, G.S. / Betzel, C. / Ealick, S.E. / Mikhailov, A.M.
CitationJournal: To be Published
Title: Crystal Structures of Salmonella Typhimurium Uridine Phosphorylase in Native and Three Complexes Forms - with Uridine, Uracil and Sulfate.
Authors: Gabdoulkhakov, A.G. / Dontsova, M.V. / Kachalova, G.S. / Betzel, C. / Ealick, S.E. / Mikhailov, A.M.
History
DepositionNov 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,72311
Polymers163,0156
Non-polymers7085
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21850 Å2
ΔGint-201 kcal/mol
Surface area43900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.370, 123.730, 134.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uridine phosphorylase / / UrdPase / UPase


Mass: 27169.092 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: UDP / Plasmid: PBLUESCRIPT IISK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P0A1F6, uridine phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 4000, SODIUM-ACETATE TRIHYDRATE, uridine-5p-monophosphate, ammonium sulphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8043 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8043 Å / Relative weight: 1
ReflectionResolution: 2.35→28.66 Å / Num. obs: 60846 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.53
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.23 / Num. unique all: 3728 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
MOLREPV. 7.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SJ9

1sj9


Resolution: 2.35→28.66 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3750350.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3020 5 %RANDOM
Rwork0.194 ---
all0.196 ---
obs0.194 60438 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.9424 Å2 / ksol: 0.389313 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.35→28.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10912 0 41 207 11160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it6.151.5
X-RAY DIFFRACTIONc_mcangle_it8.92
X-RAY DIFFRACTIONc_scbond_it8.522
X-RAY DIFFRACTIONc_scangle_it11.042.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 503 5 %
Rwork0.27 9528 -
obs-10031 98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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