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- PDB-1zl2: Crystal structure of the uridine phosphorylase from Salmonella ty... -

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Basic information

Entry
Database: PDB / ID: 1zl2
TitleCrystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with 2,2'-anhydrouridine and phosphate ion at 1.85A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside metabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / cytosol / cytoplasm
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
2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil / PHOSPHATE ION / Uridine phosphorylase / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGabdoulkhakov, A.G. / Dontsova, M.V. / Lashkov, A.A. / Betzel, C. / Ealick, S. / Mikhailov, A.M.
CitationJournal: To be Published
Title: Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with inhibitor and phosphate ion at 1.85A resolution
Authors: Gabdoulkhakov, A.G. / Dontsova, M.V. / Lashkov, A.A. / Betzel, C. / Ealick, S. / Mikhailov, A.M.
History
DepositionMay 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: 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 1.4Oct 18, 2017Group: Structure summary / Category: entity
Item: _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description
Revision 1.5Aug 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)163,97812
Polymers163,0156
Non-polymers9636
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22360 Å2
ΔGint-121 kcal/mol
Surface area43690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.790, 124.070, 134.110
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 in the asymmetric unit

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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: O33808, UniProt: P0A1F6*PLUS, uridine phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ANU / 2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil / Anhydrouridine / 2,2'-ANHYDROURIDINE / CYCLOURIDINE


Mass: 226.186 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H10N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 2.39 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 4000, SODIUM-ACETATE TRIHYDRATE, 2,2'-ANHYDROURIDINE, SODIUM PHOSPHATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 1.85→28.09 Å / Num. obs: 120586 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.25 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.079 / Net I/σ(I): 11.24
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.55 / Num. unique all: 20054 / Rsym value: 0.36 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
MOLREPV. 7.5.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SJ9

1sj9


Resolution: 1.85→28.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3429974.78 / 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
Rfree0.198 6010 5 %RANDOM
Rwork0.178 ---
all0.179 ---
obs0.178 120586 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6093 Å2 / ksol: 0.356719 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å20 Å2
2---1.09 Å20 Å2
3----1.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10951 0 63 642 11656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it4.851.5
X-RAY DIFFRACTIONc_mcangle_it6.412
X-RAY DIFFRACTIONc_scbond_it7.732
X-RAY DIFFRACTIONc_scangle_it9.852.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 1005 5 %
Rwork0.248 19049 -
obs-19049 96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2anu.paramanu.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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