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- PDB-3o6v: Crystal structure of Uridine Phosphorylase from Vibrio cholerae O... -

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Basic information

Entry
Database: PDB / ID: 3o6v
TitleCrystal structure of Uridine Phosphorylase from Vibrio cholerae O1 biovar El Tor
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich / uridine phosphorylation
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / 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
FORMIC ACID / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsMaltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of Uridine Phosphorylase from Vibrio cholerae O1 biovar El Tor
Authors: Maltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,1605
Polymers55,9302
Non-polymers2303
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-24 kcal/mol
Surface area18810 Å2
MethodPISA
2
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)168,48115
Polymers167,7906
Non-polymers6919
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 area22240 Å2
ΔGint-127 kcal/mol
Surface area47760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.074, 93.074, 155.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Uridine phosphorylase /


Mass: 27964.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_1034 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q9KT71, uridine phosphorylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 16 % PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 55546 / Num. obs: 55546 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 15.48 Å2 / Rsym value: 0.163 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 2728 / Rsym value: 0.474 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
BALBESphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1lx7

1lx7


Resolution: 1.695→35.784 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2808 5.08 %RANDOM
Rwork0.148 ---
all0.149 55250 --
obs0.149 55250 99.14 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.919 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.438 Å2-0 Å20 Å2
2---7.438 Å20 Å2
3---14.8759 Å2
Refinement stepCycle: LAST / Resolution: 1.695→35.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 15 600 4364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084082
X-RAY DIFFRACTIONf_angle_d1.1555567
X-RAY DIFFRACTIONf_dihedral_angle_d12.9591533
X-RAY DIFFRACTIONf_chiral_restr0.078648
X-RAY DIFFRACTIONf_plane_restr0.004732
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6955-1.75610.26122780.23295132551097
1.7561-1.82640.22252990.18395215551499
1.8264-1.90950.18192780.1535220549899
1.9095-2.01020.2132820.14935266554899
2.0102-2.13610.16362830.142152685551100
2.1361-2.3010.17682750.14265244551999
2.301-2.53250.17732660.14135296556299
2.5325-2.89880.19823050.14735230553599
2.8988-3.65170.15872740.140952845558100
3.6517-35.79220.15522680.13865287555599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14010.1246-0.13540.292-0.00380.2911-0.00280.02370.004-0.00480.00440.09250.0279-0.0619-0.00440.0406-0.0068-0.00280.06110.00440.071425.33858.4716-1.8925
20.3785-0.0670.04920.17410.0910.31440.017-0.02060.01030.0076-0.01070.05980.011-0.0726-0.00180.015-0.00530.00580.03950.00070.030119.109332.82652.6572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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