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- PDB-5m2t: X-ray structure of uridine phosphorylase from Vibrio cholerae in ... -

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Basic information

Entry
Database: PDB / ID: 5m2t
TitleX-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 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
URIDINE / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.03 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
RFBR14-04-00952a Russian Federation
Grant of President of Russian FederationMK-9246.2016.3 Russian Federation
CitationJournal: To Be Published
Title: X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdulkhakov, A.G. / Dontsova, M.V. / Betzel, C. / Mikhailov, A.M.
History
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)164,48723
Polymers162,6546
Non-polymers1,83317
Water31,5081749
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25710 Å2
ΔGint-216 kcal/mol
Surface area45740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.323, 72.039, 89.193
Angle α, β, γ (deg.)110.560, 107.530, 85.830
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, udp_1, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_ ...Gene: udp, udp_1, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, 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 , 6 types, 1766 molecules

#2: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1749 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
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: 0.886 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.03→79.792 Å / Num. all: 658820 / Num. obs: 658820 / % possible obs: 93.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.55 Å2 / Rpim(I) all: 0.05 / Rrim(I) all: 0.094 / Rsym value: 0.079 / Net I/av σ(I): 4.9 / Net I/σ(I): 8.5 / Num. measured all: 2282101
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.03-1.093.50.8720.9320758922380.5461.0320.8721.789.3
1.09-1.153.30.5181.4293795888010.3360.620.5182.990.9
1.15-1.233.60.3652301384846060.2260.4310.3654.292.2
1.23-1.333.50.2712.4283587802170.1680.320.2715.693.7
1.33-1.463.50.1783.7259094742800.1120.2110.1787.294.6
1.46-1.633.60.1096.2247229678620.0670.1280.10910.495.5
1.63-1.883.40.0739.2201548598620.0470.0880.07313.795.6
1.88-2.33.50.05611.3176716509310.0350.0660.05619.196.2
2.3-3.263.30.05111.5128262387850.0330.0610.05121.895
3.26-46.2063.30.04713.369728212380.030.0560.04724.194.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.533
Highest resolutionLowest resolution
Rotation46.21 Å2.5 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6O

4k6o


Resolution: 1.03→44.462 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 12.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1374 6558 1 %
Rwork0.1177 652201 -
obs0.1179 658759 93.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.21 Å2 / Biso mean: 16.6091 Å2 / Biso min: 4.85 Å2
Refinement stepCycle: final / Resolution: 1.03→44.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11285 0 20 1762 13067
Biso mean--29.29 33.61 -
Num. residues----1515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313466
X-RAY DIFFRACTIONf_angle_d1.35618478
X-RAY DIFFRACTIONf_chiral_restr0.1052113
X-RAY DIFFRACTIONf_plane_restr0.0092474
X-RAY DIFFRACTIONf_dihedral_angle_d23.4985187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.03-1.04170.24822090.2622206872089689
1.0417-1.0540.26682010.2482206702087189
1.054-1.06680.23262090.2356207802098989
1.0668-1.08030.24062170.2274210142123190
1.0803-1.09450.232090.2136211952140491
1.0945-1.10950.21112020.2005211862138891
1.1095-1.12540.20422090.1892211832139291
1.1254-1.14220.19332170.1737211892140691
1.1422-1.160.18982170.1633213562157391
1.16-1.17910.17662210.1482213712159292
1.1791-1.19940.15012360.1353214612169792
1.1994-1.22120.14692260.127216762190293
1.2212-1.24470.12752130.1185216022181593
1.2447-1.27010.14862260.1126218352206194
1.2701-1.29770.1282150.1087219032211894
1.2977-1.32790.13022480.1044219372218594
1.3279-1.36110.12882160.1003219172213394
1.3611-1.39790.10811920.0938221302232295
1.3979-1.43910.11012430.0882220672231095
1.4391-1.48550.10922480.0865221322238095
1.4855-1.53860.10342290.0867223582258795
1.5386-1.60020.10432150.0858223112252696
1.6002-1.6730.12582090.0896222782248796
1.673-1.76120.10922050.0954223452255096
1.7612-1.87160.11562260.0999221892241595
1.8716-2.01610.12792140.1027224052261996
2.0161-2.2190.11932060.1053225132271996
2.219-2.54010.13242130.111224852269897
2.5401-3.20010.14362450.1176220112225694
3.2001-44.5030.12962220.1146220152223795

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