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- PDB-4ogk: X-ray structure of the uridine phosphorylase from Salmonella typh... -

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Basic information

Entry
Database: PDB / ID: 4ogk
TitleX-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossman Fold / phosphat-ion / pirimidine nucleozide
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / 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
ISOPROPYL ALCOHOL / : / DI(HYDROXYETHYL)ETHER / THYMIDINE / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSotnichenko, S.E. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Mikhailov, A.M.
CitationJournal: To be Published
Title: X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution
Authors: Sotnichenko, S.E. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Mikhailov, A.M.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _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.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_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)164,87419
Polymers163,0156
Non-polymers1,85913
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24060 Å2
ΔGint-99 kcal/mol
Surface area48760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.970, 89.970, 256.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailscontent of asymmetric unit is biological assembly

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Uridine phosphorylase / UPase / UrdPase


Mass: 27169.092 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM3968, STMD1.21, udp / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1F6, uridine phosphorylase

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Non-polymers , 7 types, 69 molecules

#2: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N2O5
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.84 Å3/Da / Density % sol: 33.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 40% (w/v) polyethylene glycol 3350, 0.1 M Tris-maleate-NaOH, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2012
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.48
ReflectionResolution: 2.4→20 Å / Num. all: 45188 / Num. obs: 45188 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 16.33
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.4-2.552.38194343900199.1
2.55-2.723.651494329681100
2.72-2.936.361371527111100
2.93-3.2110.231300625511100
3.21-3.5718.44227074437199.9
3.57-4.128.931975338321100
4.1-4.9738.16172163337199.7
4.97-6.8139.29148032861199.5
6.81-2045.19129372493195
69321134691
2452048171
1094121291
855316611
31926191
27445451

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4IP0

4ip0


Resolution: 2.4→9.993 Å / FOM work R set: 0.7761 / σ(F): 2.5 / Phase error: 29.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 2242 5.09 %random
Rwork0.2197 ---
obs0.2228 44056 97.69 %-
all-44056 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.49 Å2 / Biso mean: 59.31 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.4→9.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11222 0 126 56 11404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111521
X-RAY DIFFRACTIONf_angle_d1.05915615
X-RAY DIFFRACTIONf_chiral_restr0.0761845
X-RAY DIFFRACTIONf_plane_restr0.0072007
X-RAY DIFFRACTIONf_dihedral_angle_d15.0394157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4002-2.45170.38961330.38752513264690
2.4517-2.50780.40481370.36412567270490
2.5078-2.56950.38111290.33952557268691
2.5695-2.63770.35351300.33082544267491
2.6377-2.71380.35011360.30942512264890
2.7138-2.79950.30971380.28852628276692
2.7995-2.89720.30371370.27652599273692
2.8972-3.01010.29171380.26422585272392
3.0101-3.1430.26631390.26022608274794
3.143-3.30290.29211420.24172674281694
3.3029-3.50140.26891400.22432656279695
3.5014-3.75820.20051410.2142684282595
3.7582-4.11190.17721420.19752691283395
4.1119-4.65290.20881390.1682645278495
4.6529-5.67530.15991420.18062691283395
5.6753-9.95330.20531410.17152671281294

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