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- PDB-4r2w: X-ray structure of uridine phosphorylase from Shewanella oneidens... -

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Basic information

Entry
Database: PDB / ID: 4r2w
TitleX-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 in complex with uridine at 1.6 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Uridine phosphorylase / Uridine Binding
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / 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 / Uridine phosphorylase
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSafonova, T.N. / Mordkovich, N.N. / Manuvera, V.A. / Veiko, V.P. / Popov, V.O. / Polyakov, K.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine.
Authors: Safonova, T.N. / Mikhailov, S.N. / Veiko, V.P. / Mordkovich, N.N. / Manuvera, V.A. / Alekseev, C.S. / Kovalchuk, M.V. / Popov, V.O. / Polyakov, K.M.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionDec 10, 2014ID: 4HER
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Sep 20, 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)162,83121
Polymers161,2666
Non-polymers1,56515
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25290 Å2
ΔGint-264 kcal/mol
Surface area42070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.920, 96.480, 91.930
Angle α, β, γ (deg.)90.00, 120.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uridine phosphorylase


Mass: 26877.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: udp, SO_4133 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8E9X9, uridine phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.75M ammonium sulfate, 0.075M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP , temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.812 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 8, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.523
11-H-L, K, H20.318
11L, K, -H-L30.159
ReflectionResolution: 1.6→79.62 Å / Num. all: 205488 / Num. obs: 171553 / % possible obs: 77.3 % / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1rxy

1rxy


Resolution: 1.6→19.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.421 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: refinement against detwinned data
RfactorNum. reflection% reflectionSelection details
Rfree0.19188 8948 5.1 %RANDOM
Rwork0.17729 ---
obs0.17805 165794 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.451 Å2
Baniso -1Baniso -2Baniso -3
1--14.8 Å2-0 Å2-2.94 Å2
2--28.87 Å20 Å2
3----14.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10850 0 93 554 11497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01911175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.95715199
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68451453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59723.501437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.036151741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1421576
X-RAY DIFFRACTIONr_chiral_restr0.1360.21814
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218331
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3181.6425845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.792.4627287
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8111.7845330
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.3514.20317411
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 670 -
Rwork0.256 12332 -
obs--95.77 %

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