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- PDB-1oty: Native PNP +ALLO -

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Basic information

Entry
Database: PDB / ID: 1oty
TitleNative PNP +ALLO
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / DNA damage response / identical protein binding / membrane / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / 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
6-METHYLPURINE / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEalick, S.E. / Bennett, E.M. / Anand, R. / Secrist, J.A. / Parker, W.B. / Hassan, A.E. / Allan, P.W. / McPherson, D.T. / Sorscher, E.J.
CitationJournal: Chem.Biol. / Year: 2003
Title: Designer gene therapy using an Escherichia coli purine nucleoside phosphorylase/prodrug system.
Authors: Bennett, E.M. / Anand, R. / Allan, P.W. / Hassan, A.E. / Hong, J.S. / Levasseur, D.N. / McPherson, D.T. / Parker, W.B. / Secrist, J.A. / Sorscher, E.J. / Townes, T.M. / Waud, W.R. / Ealick, S.E.
History
DepositionMar 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2409
Polymers77,5523
Non-polymers6876
Water3,135174
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,47918
Polymers155,1046
Non-polymers1,37512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area24690 Å2
ΔGint-147 kcal/mol
Surface area44470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.970, 119.970, 240.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Purine nucleoside phosphorylase / Inosine phosphorylase / PNP


Mass: 25850.748 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-6MP / 6-METHYLPURINE


Mass: 134.139 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.19 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 50mM sodium citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mM1droppH8.0KH2PO4
235 mg/mlprotein1drop
330 %ammonium sulfate1reservoir
450 mMcitrate1reservoirpH5.4

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.5→26.2 Å / Num. all: 36116 / Num. obs: 36116 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.9
Reflection shellHighest resolution: 2.5 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 7.9 / Num. unique all: 4151 / Rsym value: 0.079 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.2 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3603 10 %RANDOM
Rwork0.203 ---
obs0.203 36116 99.9 %-
all-36116 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8447 Å2 / ksol: 0.381305 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å23.17 Å20 Å2
2--3.32 Å20 Å2
3----6.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.5→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 45 174 5598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 596 10.2 %
Rwork0.248 5275 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4BAS.PAR
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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