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- PDB-5c80: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -

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Basic information

Entry
Database: PDB / ID: 5c80
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / metal ion binding / 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
DI(HYDROXYETHYL)ETHER / URIDINE / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.243 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR14-04-00952a Russian Federation
CitationJournal: Crystallography Reports / Year: 2016
Title: X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Balaev, V.V. / Seregina, T.A. / Mironov, A.S. / Betzel, C. / Mikhailov, A.M.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)166,07235
Polymers162,6546
Non-polymers3,41829
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29600 Å2
ΔGint-142 kcal/mol
Surface area44140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.255, 73.110, 83.137
Angle α, β, γ (deg.)71.810, 77.190, 85.690
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Uridine phosphorylase


Mass: 27108.994 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: udp, DN30_1909, VC39_02535, VC78_02550, VS27_10630, WG08_05660
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

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Non-polymers , 7 types, 851 molecules

#2: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97989 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 2.243→77.231 Å / Num. all: 58293 / Num. obs: 58293 / % possible obs: 91.1 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.055 / Rrim(I) all: 0.077 / Net I/av σ(I): 11.229 / Net I/σ(I): 9.6 / Num. measured all: 101646
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.243-2.361.70.3332.31327178100.3330.3332.383.2
2.36-2.511.80.2183.41479881930.2180.2183.693.2
2.51-2.681.70.1455.11380079130.1450.1454.895.1
2.68-2.91.70.0977.51239673530.0970.0976.794.9
2.9-3.171.80.0710.41234168090.070.079.195.4
3.17-3.551.70.0514.31039659980.050.0512.493.2
3.55-4.11.70.03519.2827147850.0350.03517.184.4
4.1-5.021.80.0320.3723841100.030.032186.3
5.02-7.091.70.03120.1594034550.0310.03120.792.8
7.09-45.4271.70.02619319518670.0260.02626.492.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.03 Å45.43 Å
Translation8.03 Å45.43 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LWZ

4lwz


Resolution: 2.243→45.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2136 / WRfactor Rwork: 0.1515 / FOM work R set: 0.8352 / SU B: 7.17 / SU ML: 0.174 / SU R Cruickshank DPI: 0.5856 / SU Rfree: 0.2644 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.586 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2849 4.9 %RANDOM
Rwork0.1683 ---
obs0.1716 55318 90.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.62 Å2 / Biso mean: 30.999 Å2 / Biso min: 3.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.04 Å20.08 Å2
2---0.17 Å20.01 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.243→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11263 0 167 822 12252
Biso mean--29.06 37.85 -
Num. residues----1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911757
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.97715933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20451514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20523.747459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.511151935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1461580
X-RAY DIFFRACTIONr_chiral_restr0.1180.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218628
X-RAY DIFFRACTIONr_mcbond_it1.5462.9416050
X-RAY DIFFRACTIONr_mcangle_it2.5394.4017538
X-RAY DIFFRACTIONr_scbond_it1.8723.1375707
LS refinement shellResolution: 2.243→2.301 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 173 -
Rwork0.278 3297 -
all-3470 -
obs--72.91 %

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