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- PDB-4r2x: Unique conformation of uridine and asymmetry of the hexameric mol... -

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Basic information

Entry
Database: PDB / ID: 4r2x
TitleUnique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine
Componentsuridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase
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 phosphorylase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsSafonova, T.N. / Mordkovich, N.N. / Manuvera, V.A. / Veiko, V.P. / Popov, V.O. / Polyakov, K.M.
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: 4HEN
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 / 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
C: uridine phosphorylase
D: uridine phosphorylase
E: uridine phosphorylase
F: uridine phosphorylase
A: uridine phosphorylase
B: uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,92637
Polymers161,2666
Non-polymers2,66031
Water19,6721092
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29860 Å2
ΔGint-314 kcal/mol
Surface area39580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.540, 95.930, 91.610
Angle α, β, γ (deg.)90.00, 120.00, 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 (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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1092 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 0.75M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, temperature 293K, FREE INTERFACE DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.8
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.802
11-H-L, K, H20.1
11L, K, -H-L30.098
ReflectionResolution: 0.93→79.35 Å / Num. obs: 883288 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.126 / Rsym value: 0.87 / Net I/σ(I): 12.2
Reflection shellResolution: 0.95→1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.708 / % possible all: 93.4

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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: 1RXY

1rxy


Resolution: 0.93→29.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.423 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.004 / ESU R Free: 0.004 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.164 43368 4.9 %RANDOM
Rwork0.149 ---
obs0.15 834827 95.9 %-
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: 8.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å2-0 Å21.68 Å2
2--10.97 Å20 Å2
3----8.36 Å2
Refinement stepCycle: LAST / Resolution: 0.93→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10834 0 158 1092 12084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210739
X-RAY DIFFRACTIONr_angle_refined_deg1.691.96215492
X-RAY DIFFRACTIONr_angle_other_deg0.919324600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46651464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62823.833454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.115151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0321574
X-RAY DIFFRACTIONr_chiral_restr0.1010.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022461
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_it0.9880.9575888
X-RAY DIFFRACTIONr_mcbond_other0.98817.3215887
X-RAY DIFFRACTIONr_mcangle_it1.2487342
X-RAY DIFFRACTIONr_mcangle_other1.2487343
X-RAY DIFFRACTIONr_scbond_it1.4235522
X-RAY DIFFRACTIONr_scbond_other1.4235517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.648145
X-RAY DIFFRACTIONr_long_range_B_refined2.04913421
X-RAY DIFFRACTIONr_long_range_B_other2.04913420
X-RAY DIFFRACTIONr_rigid_bond_restr4.586311377
X-RAY DIFFRACTIONr_sphericity_free20.2385225
X-RAY DIFFRACTIONr_sphericity_bonded7.518512006
LS refinement shellResolution: 0.93→0.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 3001 -
Rwork0.24 58025 -
obs--89.99 %

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