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- PDB-3dps: X-ray structure of the unliganded uridine phosphorylase from salm... -

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Basic information

Entry
Database: PDB / ID: 3dps
TitleX-ray structure of the unliganded uridine phosphorylase from salmonella typhimurium in homodimeric form at 1.8A
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homology
Function and homology information


nucleoside catabolic process / uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine phosphorylase activity / 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 phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMikhailov, A.M. / Lashkov, A.A.
CitationJournal: To be Published
Title: X-ray structure of the unliganded uridine phosphorylase from salmonella typhimurium in homodimeric form at 1.8A
Authors: Lashkov, A.A. / Mikhailov, A.M.
History
DepositionJul 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4303
Polymers54,3382
Non-polymers921
Water4,576254
1
A: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules

A: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules

A: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2919
Polymers163,0156
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area17510 Å2
ΔGint-113 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.860, 150.860, 47.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: 1-y, x-y, z and 1-x+y, x-1, z.

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Components

#1: Protein Uridine phosphorylase / / UrdPase / UPase


Mass: 27169.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: udp / Plasmid: PBLUESCRIPT IISK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3 / References: UniProt: P0A1F6, uridine phosphorylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.93 Å3/Da / Density % sol: 36.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 400, NaN3, GLYCEROL, 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: 0.813 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 23, 2007
RadiationMonochromator: GAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 37630 / Num. obs: 37497 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.14 Å2 / Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
EMBLdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OXF

2oxf


Resolution: 1.8→18.696 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.21 / σ(F): 2.01 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1874 5 %
Rwork0.161 35621 -
obs0.163 37495 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.232 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 162.77 Å2 / Biso mean: 25.463 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.399 Å2-0 Å20 Å2
2---0.399 Å2-0 Å2
3---0.798 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 6 254 3808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063622
X-RAY DIFFRACTIONf_angle_d1.0424911
X-RAY DIFFRACTIONf_chiral_restr0.071587
X-RAY DIFFRACTIONf_plane_restr0.004632
X-RAY DIFFRACTIONf_dihedral_angle_d15.1691300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8490.2411440.16827362880100
1.849-1.9030.2621440.16527522896100
1.903-1.9640.1911460.17227662912100
1.964-2.0340.2161420.16127032845100
2.034-2.1160.2071470.15627812928100
2.116-2.2120.21440.15527462890100
2.212-2.3280.2151440.16527392883100
2.328-2.4740.2181440.1627332877100
2.474-2.6640.2031450.16127552900100
2.664-2.9320.1991450.16727462891100
2.932-3.3540.2151440.16527432887100
3.354-4.2180.1711450.13827482893100
4.218-18.6970.151400.1492673281397

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