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- PDB-4lnh: Crystal structure of uridine phosphorylase from Vibrio fischeri E... -

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Basic information

Entry
Database: PDB / ID: 4lnh
TitleCrystal structure of uridine phosphorylase from Vibrio fischeri ES114, NYSGRC Target 29520.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


uridine phosphorylase / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol
Similarity search - Function
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 speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsMalashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. ...Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of uridine phosphorylase from Vibrio fischeri ES114, NYSGRC Target 29520.
Authors: Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. ...Authors: Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Almo, S.C.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0183
Polymers29,8291
Non-polymers1882
Water93752
1
A: Uridine phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)180,10618
Polymers178,9776
Non-polymers1,12912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area17290 Å2
ΔGint-222 kcal/mol
Surface area51100 Å2
MethodPISA
2
A: Uridine phosphorylase
hetero molecules

A: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0356
Polymers59,6592
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3680 Å2
ΔGint-59 kcal/mol
Surface area19120 Å2
MethodPISA
3
A: Uridine phosphorylase
hetero molecules

A: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0356
Polymers59,6592
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area2790 Å2
ΔGint-54 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.732, 164.732, 58.168
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-614-

HOH

Detailsdimeric

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Components

#1: Protein Uridine phosphorylase


Mass: 29829.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: 3280420, VF_A0530 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q5E046, uridine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium sulfate, 0.1 M HEPES:NaOH, pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13419 / % possible obs: 99.4 % / Redundancy: 11 % / Rmerge(I) obs: 0.073 / Χ2: 1.594 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3411.20.7136670.9511100
2.34-2.3811.20.5416570.9571100
2.38-2.4311.20.426920.9871100
2.43-2.4811.30.386510.9951100
2.48-2.5311.30.3176631.0031100
2.53-2.5911.30.2736661.0571100
2.59-2.6611.30.236871.0921100
2.66-2.7311.30.1966621.1231100
2.73-2.8111.30.1536641.208199.8
2.81-2.911.20.1266781.3381100
2.9-311.50.1056641.473199.8
3-3.1211.40.0896761.459199.9
3.12-3.2611.40.086651.582199.7
3.26-3.4411.40.0666861.84199.7
3.44-3.65100.0666652.068199.4
3.65-3.9310.10.076682.405198.5
3.93-4.33110.0626672.402198.7
4.33-4.9510.60.0536722.717198.7
4.95-6.249.90.056843.145198.8
6.24-5010.10.0566852.582195.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QPB

3qpb


Resolution: 2.3→31.13 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.1708 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8531 / SU B: 10.521 / SU ML: 0.126 / SU R Cruickshank DPI: 0.0518 / SU Rfree: 0.0409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 663 5 %RANDOM
Rwork0.1698 ---
obs0.1719 13369 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.85 Å2 / Biso mean: 61.6326 Å2 / Biso min: 38.06 Å2
Baniso -1Baniso -2Baniso -3
1--35.51 Å2-0 Å2-0 Å2
2---35.51 Å2-0 Å2
3---71.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 11 52 1907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191881
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.972544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83424.94387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06715304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9481510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021408
X-RAY DIFFRACTIONr_mcbond_it3.0457.3954
X-RAY DIFFRACTIONr_mcangle_it4.80998.121189
X-RAY DIFFRACTIONr_scbond_it3.6777.693926
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 51 -
Rwork0.272 914 -
all-965 -
obs--98.47 %
Refinement TLS params.Method: refined / Origin x: 1.2334 Å / Origin y: 29.6138 Å / Origin z: 26.9973 Å
111213212223313233
T0.2295 Å2-0.0097 Å2-0.0108 Å2-0.1569 Å20.0202 Å2--0.0412 Å2
L1.1678 °20.2131 °2-0.0435 °2-1.4899 °2-0.0528 °2--0.4511 °2
S-0.0059 Å °0.0681 Å °0.1644 Å °-0.018 Å °-0.0007 Å °0.1849 Å °-0.1458 Å °0.024 Å °0.0066 Å °

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