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- PDB-5lhv: X-ray structure of uridine phosphorylase from Vibrio cholerae in ... -

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Basic information

Entry
Database: PDB / ID: 5lhv
TitleX-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 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
URACIL / URIDINE / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.288 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Balaev, V.V. / Betzel, C. / Mikhailov, A.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR14-04-00952a Russian Federation
CitationJournal: To Be Published
Title: X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 A resolution
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Balaev, V.V. / Betzel, C. / Mikhailov, A.M.
History
DepositionJul 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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)165,26349
Polymers161,2606
Non-polymers4,00343
Water28,5721586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32300 Å2
ΔGint-402 kcal/mol
Surface area42310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.223, 71.648, 88.878
Angle α, β, γ (deg.)69.700, 72.700, 86.240
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: 26876.693 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: udp, udp_1, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

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Non-polymers , 8 types, 1629 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H12N2O6
#4: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H4N2O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1586 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.288→46.23 Å / Num. obs: 337058 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 10.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.288-1.370.6821.680.766189.8
1.37-1.460.4612.610.961192.5
1.46-1.580.2814.130.949192.9
1.58-1.730.1676.90.976194.7
1.73-1.930.09910.940.989195
1.93-2.230.05719.490.996196
2.23-2.730.03827.490.998196.4
2.73-3.850.02443.140.999197.7
3.85-46.233.40.01955.160.999198

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.525
Highest resolutionLowest resolution
Rotation44.38 Å2.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6O

4k6o


Resolution: 1.288→33.569 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 20.29
RfactorNum. reflection% reflection
Rfree0.1783 3531 1.05 %
Rwork0.145 --
obs0.1454 336588 93.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.01 Å2 / Biso mean: 22.24 Å2 / Biso min: 7.15 Å2
Refinement stepCycle: final / Resolution: 1.288→33.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11233 0 248 1587 13068
Biso mean--19.55 37.74 -
Num. residues----1503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412208
X-RAY DIFFRACTIONf_angle_d1.63316608
X-RAY DIFFRACTIONf_chiral_restr0.11956
X-RAY DIFFRACTIONf_plane_restr0.0082143
X-RAY DIFFRACTIONf_dihedral_angle_d14.5864575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2884-1.30610.35551260.3242118911201784
1.3061-1.32470.31781380.2544129921313092
1.3247-1.34450.2321390.2335130491318892
1.3445-1.36550.29711380.2402130191315792
1.3655-1.38790.27391370.2495127891292691
1.3879-1.41180.23991400.2014131931333393
1.4118-1.43750.22351400.1928131831332393
1.4375-1.46510.21641390.205131381327793
1.4651-1.49510.23971380.204130911322992
1.4951-1.52760.25341370.2031129891312691
1.5276-1.56310.21791410.1568132751341694
1.5631-1.60220.18911420.1372133911353394
1.6022-1.64550.18461420.1336133911353395
1.6455-1.69390.2011440.1268135191366395
1.6939-1.74860.16981440.1266135481369295
1.7486-1.81110.16691430.127134771362096
1.8111-1.88360.14371440.126135781372296
1.8836-1.96930.17191380.1373133111344994
1.9693-2.07310.1771430.1284135611370495
2.0731-2.2030.14261450.1214136751382097
2.203-2.3730.17591440.1298135911373596
2.373-2.61180.18021470.1293137771392497
2.6118-2.98950.16531460.1377138121395897
2.9895-3.76560.15011480.1227138851403398
3.7656-33.58010.13831480.1308139321408098

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