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- PDB-1t0u: Crystal structure of E.coli uridine phosphorylase at 2.2 A resolu... -

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Basic information

Entry
Database: PDB / ID: 1t0u
TitleCrystal structure of E.coli uridine phosphorylase at 2.2 A resolution (Type-A Native)
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / PENTOSYLTRANSFERASE / URIDINE PHOSPHORYLASE
Function / homology
Function and homology information


UMP catabolic process / uridine catabolic process / uridine phosphorylase / 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
Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIR(URANYL DERIVATIVE) / Resolution: 2.2 Å
AuthorsCaradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium
Authors: Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F.
History
DepositionApr 13, 2004Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 27, 2004ID: 1LGG
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)54,3782
Polymers54,3782
Non-polymers00
Water4,450247
1
A: Uridine phosphorylase
B: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)163,1346
Polymers163,1346
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15630 Å2
ΔGint-120 kcal/mol
Surface area47370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.336, 151.336, 48.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a hexamer.THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Components

#1: Protein Uridine phosphorylase / UrdPase / UPase


Mass: 27189.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PPROEX::PVDS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12758, uridine phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.02 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, PEG, Sodium Acetate, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 5, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→29.11 Å / Num. all: 188478 / Num. obs: 20914 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 3.77 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.08
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.42 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5refinement
RefinementMethod to determine structure: SIR(URANYL DERIVATIVE) / Resolution: 2.2→29.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.319 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1075 5.1 %RANDOM
Rwork0.161 ---
all0.163 20914 --
obs0.163 19837 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.25 Å20 Å2
2---0.51 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 0 247 3758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213566
X-RAY DIFFRACTIONr_bond_other_d00.023342
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9524843
X-RAY DIFFRACTIONr_angle_other_deg1.45237738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1563470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40415614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023989
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02681
X-RAY DIFFRACTIONr_nbd_refined0.2220.3909
X-RAY DIFFRACTIONr_nbd_other0.2370.33587
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.050.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5334
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1110.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.376
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.971.52344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7923764
X-RAY DIFFRACTIONr_scbond_it2.79531222
X-RAY DIFFRACTIONr_scangle_it4.6244.51079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 75
Rwork0.172 1447

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