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- PDB-2hrd: Crystal structure of the uridine phosphorylase from Salmonella ty... -

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Basic information

Entry
Database: PDB / ID: 2hrd
TitleCrystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / 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
PHOSPHATE ION / THYMINE / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTimofeev, V.I. / Gabdulkhakov, A.G. / Mikhailov, A.M.
CitationJournal: To be Published
Title: Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution
Authors: Timofeev, V.I. / Gabdulkhakov, A.G. / Mikhailov, A.M. / Dontsova, M.V. / Voelter, W. / Betzel, C.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,23026
Polymers163,0156
Non-polymers2,21520
Water12,701705
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26970 Å2
ΔGint-167 kcal/mol
Surface area42760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.200, 123.400, 133.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hexamer, which presented in the asymmetric unit.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 5 types, 725 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 297 K
Details: 25% PEG 400, 0.1M potassium phosphate, 0.2M magnesium chloride, 0.1M cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 15, 2005 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 159741
Reflection shellResolution: 1.7→1.74 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZL2

1zl2


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.57 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18883 7980 5 %RANDOM
Rwork0.1663 ---
obs0.16742 151618 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11116 0 140 705 11961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02212132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.97516565
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55851656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4323.765502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.033152099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3261595
X-RAY DIFFRACTIONr_chiral_restr0.0710.21925
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029125
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.27233
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.28427
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.21152
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4911.57824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.826212406
X-RAY DIFFRACTIONr_scbond_it0.97234757
X-RAY DIFFRACTIONr_scangle_it1.6114.54069
X-RAY DIFFRACTIONr_rigid_bond_restr0.592312581
X-RAY DIFFRACTIONr_sphericity_free1.6953709
X-RAY DIFFRACTIONr_sphericity_bonded0.828311875
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 582 -
Rwork0.187 11047 -
obs--100 %

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