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- PDB-1ryz: Uridine Phosphorylase from Salmonella typhimurium. Crystal Struct... -

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Basic information

Entry
Database: PDB / ID: 1ryz
TitleUridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / 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
ACETIC ACID / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDontsova, M.V. / Gabdoulkhakov, A.G. / Lyashenko, A.V. / Nikonov, S.V. / Ealick, S.E. / Mikhailov, A.M.
CitationJournal: TO BE PUBLISHED
Title: Structure-functions studies of uridine phosphorylase from Salmonella typhimurium
Authors: Dontsova, M.V. / Gabdoulkhakov, A.G. / Lyashenko, A.V. / Nikonov, S.V. / Ealick, S.E. / Mikhailov, A.M.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / 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 / _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)163,1358
Polymers163,0156
Non-polymers1202
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uridine phosphorylase
E: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase
D: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,1358
Polymers163,0156
Non-polymers1202
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area18280 Å2
ΔGint-108 kcal/mol
Surface area51990 Å2
MethodPISA
3
B: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4584
Polymers54,3382
Non-polymers1202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
C: Uridine phosphorylase
E: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)54,3382
Polymers54,3382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.260, 92.260, 267.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2

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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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Na Acetate trihydrate, 10% PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2003 / Details: Capillary optics
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 75053 / Num. obs: 26462 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.84 % / Biso Wilson estimate: -0.2 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.177 / Net I/σ(I): 6.89
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.05 / Num. unique all: 1074 / Rsym value: 0.333 / % possible all: 75.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K3F

1k3f


Resolution: 2.9→29.46 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3363606.7 / 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
Rfree0.284 1327 5 %RANDOM
Rwork0.212 ---
all0.216 ---
obs0.212 26462 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0393 Å2 / ksol: 0.301264 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11262 0 8 0 11270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it7.941.5
X-RAY DIFFRACTIONc_mcangle_it11.792
X-RAY DIFFRACTIONc_scbond_it10.412
X-RAY DIFFRACTIONc_scangle_it13.922.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 198 4.7 %
Rwork0.211 3979 -
obs-3979 88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ACY_XPLOR.PARAMACY_XPLOR.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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