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- PDB-1tgv: Structure of E. coli Uridine Phosphorylase complexed with 5-Fluor... -

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Basic information

Entry
Database: PDB / ID: 1tgv
TitleStructure of E. coli Uridine Phosphorylase complexed with 5-Fluorouridine and sulfate
Componentsuridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / pyrimidine nucleoside phosphorylase / uridine salvage / 5-fluorouridine
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein 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
5-FLUOROURIDINE / : / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBu, W. / Settembre, E.C. / Sanders, J.M. / Begley, T.P. / Ealick, S.E.
CitationJournal: To be Published / Year: 2004
Title: Structures of E. coli Uridine Phosphorylase
Authors: Bu, W. / Settembre, E.C. / Sanders, J.M. / Begley, T.P. / Ealick, S.E.
History
DepositionMay 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: uridine phosphorylase
B: uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6987
Polymers54,9432
Non-polymers7565
Water4,828268
1
A: uridine phosphorylase
B: uridine phosphorylase
hetero molecules

A: uridine phosphorylase
B: uridine phosphorylase
hetero molecules

A: uridine phosphorylase
B: uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,09521
Polymers164,8286
Non-polymers2,26715
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area24590 Å2
ΔGint-230 kcal/mol
Surface area43380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)149.972, 149.972, 49.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3

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Components

#1: Protein uridine phosphorylase / / E.C.2.4.2.3 / UrdPase / UPase


Mass: 27471.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UDP, B3831 / Plasmid: PET28b / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P12758, uridine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-5UD / 5-FLUOROURIDINE


Mass: 262.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11FN2O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 1.93 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, MES, Glycerol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 19402 / Num. obs: 19412 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 21 Å2 / Limit h max: 58 / Limit h min: -57 / Limit k max: 67 / Limit k min: -57 / Limit l max: 22 / Limit l min: 0 / Observed criterion F max: 327031.22 / Observed criterion F min: 0.45 / Rsym value: 0.047 / Net I/σ(I): 14.4

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1862 9.9 %random
Rwork0.175 ---
all-19402 --
obs-18897 89.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 57.1813 Å2 / ksol: 0.35419 e/Å3
Displacement parametersBiso max: 66.35 Å2 / Biso mean: 28.95 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å20.05 Å20 Å2
2---3.36 Å20 Å2
3---6.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.14 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 47 268 3983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.2-2.30.2581619.80.19714810.022625164262.6
2.3-2.420.25623910.40.19720580.0172649229786.7
2.42-2.570.2362339.40.18222380.0152641247193.6
2.57-2.770.2552289.20.1922570.0172639248594.1
2.77-3.050.2492469.80.19822760.0162623252296.1
3.05-3.490.232469.80.18422660.0152615251296.1
3.49-4.390.18426610.70.15622110.0112639247793.9
4.39-19.70.2072439.80.16722480.0132628249194.8

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