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- PDB-4k6o: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -

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Basic information

Entry
Database: PDB / ID: 4k6o
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with 6-methyluracil at 1.17 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / 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
6-methylpyrimidine-2,4-diol / ETHANOL / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.17 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and preliminary X-ray study of Vibrio cholerae uridine phosphorylase in complex with 6-methyluracil.
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdulkhakov, A.G. / Dontsova, M.V. / Seregina, T.A. / Mironov, A.S. / Betzel, C. / Mikhailov, A.M.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Data collection / Database references
Revision 1.2Dec 18, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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
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)165,46860
Polymers162,6546
Non-polymers2,81454
Water44,7132482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28880 Å2
ΔGint-328 kcal/mol
Surface area45090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.012, 97.100, 93.017
Angle α, β, γ (deg.)90.00, 119.99, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Plasmid: pMZ21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

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Non-polymers , 9 types, 2536 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-6MU / 6-methylpyrimidine-2,4-diol


Mass: 126.113 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6N2O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O
#8: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2482 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 286 K / pH: 8.5
Details: PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826 Å / Relative weight: 1
ReflectionResolution: 1.17→80.56 Å / Num. obs: 449315 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.83 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.95
Reflection shellResolution: 1.17→1.2 Å / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.23 / % possible all: 55.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IP0

4ip0


Resolution: 1.17→40.28 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.07 / σ(F): 1.36 / Phase error: 10.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.128 22536 5.02 %
Rwork0.108 --
obs0.11 449273 94.1 %
all-477950 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.2 Å2
Refinement stepCycle: LAST / Resolution: 1.17→40.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11243 0 161 2482 13886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613050
X-RAY DIFFRACTIONf_angle_d1.18517980
X-RAY DIFFRACTIONf_dihedral_angle_d12.0465038
X-RAY DIFFRACTIONf_chiral_restr0.0672070
X-RAY DIFFRACTIONf_plane_restr0.0052332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.172-1.18530.16993230.1547618141
1.1853-1.19920.15875880.12891166377
1.1992-1.21380.14216850.12511339088
1.2138-1.22920.15077630.12011426495
1.2292-1.24540.13867530.11451454796
1.2454-1.26240.14198090.11141434996
1.2624-1.28050.14337450.11281464596
1.2805-1.29960.14497410.11141446096
1.2996-1.31990.13357750.1071457796
1.3199-1.34150.13647820.10721450096
1.3415-1.36470.13267460.10511450096
1.3647-1.38950.12797660.11447695
1.3895-1.41620.12147810.09821457597
1.4162-1.44510.1287520.09711473197
1.4451-1.47660.12387520.09521474897
1.4766-1.51090.1247420.09011467197
1.5109-1.54870.10777970.0861468297
1.5487-1.59060.10977560.0851472498
1.5906-1.63740.11357640.08681446295
1.6374-1.69020.10888040.09031474498
1.6902-1.75060.12348530.0931475198
1.7506-1.82070.12567980.09711472698
1.8207-1.90360.11717890.09691486898
1.9036-2.0040.12247300.09991484398
2.004-2.12950.11547750.10131461396
2.1295-2.29390.12598310.10551484598
2.2939-2.52470.12568100.10951489698
2.5247-2.890.13327520.11991486098
2.89-3.64070.13167660.11661472097
3.6407-40.30620.14078080.13571472696

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