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

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Basic information

Entry
Database: PDB / ID: 4ogl
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold / Nucleoside / phosphate ion
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
THYMINE / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.249 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: Crystallogr. Rep. / Year: 2016
Title: X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Balaev, T. / Seregina, A.S. / Mironov, C. / Betzel, C. / Mikhailov, A.M.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)164,71331
Polymers162,6546
Non-polymers2,05925
Water39,0752169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27200 Å2
ΔGint-121 kcal/mol
Surface area44990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.748, 96.499, 92.776
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 O1 biovar El Tor (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: Udp, VC_1034 / Plasmid: pMZ21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KT71, uridine phosphorylase

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Non-polymers , 6 types, 2194 molecules

#2: Chemical
ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6N2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2169 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2.6H2O, 15%(w/v) polyethylene glycol (PEG) 4000 in 0.1 M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.249→41.81 Å / Num. all: 383390 / Num. obs: 383390 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 10.56 Å2 / Rsym value: 0.065 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.25-1.3260.6991.1330285547470.69996.5
1.32-1.46.50.5271.5339110523070.52797.2
1.4-1.496.90.3482.2342245493040.34897.7
1.49-1.616.70.2133.6311773462750.21398.2
1.61-1.776.80.1325.8290320427400.13298.8
1.77-1.977.10.0819.4276944389870.08199.3
1.97-2.286.70.05513.1230229344400.05599.6
2.28-2.796.90.04415.6200931293190.04499.9
2.79-3.956.80.0320.1154037226900.03100
3.95-41.8170.02523.487580125810.02599.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4IP0

4ip0


Resolution: 1.249→7.997 Å / FOM work R set: 0.942 / SU ML: 0.1 / σ(F): 0 / Phase error: 12.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.147 19179 5.02 %random
Rwork0.1154 ---
obs0.1169 381769 98.21 %-
all-388727 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.07 Å2 / Biso mean: 16.7 Å2 / Biso min: 2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.249→7.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11243 0 137 2169 13549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812889
X-RAY DIFFRACTIONf_angle_d1.27317693
X-RAY DIFFRACTIONf_chiral_restr0.0822065
X-RAY DIFFRACTIONf_plane_restr0.0062310
X-RAY DIFFRACTIONf_dihedral_angle_d12.7825081
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.249-1.26310.24036480.2003117341238296
1.2631-1.27790.23156280.1983117281235696
1.2779-1.29350.22526290.1891118361246596
1.2935-1.30980.19826610.1636118471250897
1.3098-1.32690.18955860.1606120061259297
1.3269-1.3450.20097010.1578117811248297
1.345-1.36410.18186230.1449120011262497
1.3641-1.38440.19196120.1386118631247597
1.3844-1.40590.18186450.1317119711261697
1.4059-1.42880.16796510.1236119391259097
1.4288-1.45330.16786620.1199119791264198
1.4533-1.47960.15766500.1137119151256598
1.4796-1.50790.15266250.1068120051263098
1.5079-1.53840.14016420.0981120971273998
1.5384-1.57160.13536680.0909120521272098
1.5716-1.60790.13136140.0909120921270698
1.6079-1.64780.13236050.0897121121271798
1.6478-1.69190.13426170.0902122011281899
1.6919-1.74120.13946160.0936121251274199
1.7412-1.79680.13516380.097121271276599
1.7968-1.86030.12676330.0935123151294899
1.8603-1.93370.13116400.0956122051284599
1.9337-2.02040.11696110.0942122331284499
2.0204-2.1250.13146340.099122711290599
2.125-2.25540.13956150.10321234512960100
2.2554-2.4250.13786490.11231226812917100
2.425-2.66080.14636760.11881232212998100
2.6608-3.02740.15236880.1241235113039100
3.0274-3.74770.13676720.11571236613038100
3.7477-7.99690.14256400.12821250313143100

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