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- PDB-1tcu: Crystal Structure of the Purine Nucleoside Phosphorylase from Sch... -

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Basic information

Entry
Database: PDB / ID: 1tcu
TitleCrystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with phosphate and acetate
Componentspurine-nucleoside phosphorylasePurine nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase
Function / homology
Function and homology information


guanosine phosphorylase activity / nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / Rigid Body / Resolution: 2 Å
AuthorsPereira, H.D. / Franco, G.R. / Cleasby, A. / Garratt, R.C.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structures for the Potential Drug Target Purine Nucleoside Phosphorylase from Schistosoma mansoni Causal Agent of Schistosomiasis.
Authors: Pereira, H.D. / Franco, G.R. / Cleasby, A. / Garratt, R.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Cloning, expression and preliminary crystallographic studies of the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni
Authors: Pereira, H.M. / Cleasby, A. / Pena, S.D. / Franco, G.R. / Garratt, R.C.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)94,28812
Polymers93,5923
Non-polymers6969
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-73 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.962, 120.202, 131.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein purine-nucleoside phosphorylase / Purine nucleoside phosphorylase


Mass: 31197.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: SmPNP / Plasmid: pMal C2g / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q9BMI9, purine-nucleoside phosphorylase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.1 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 1500, Glycerol, Acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2003 / Details: mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25.82 Å / Num. obs: 50988 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Rsym value: 0.071
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.39 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Rigid Body
Starting model: SmPNP refined at 1.9 angstrons

Resolution: 2→25.82 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.201 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.226 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21329 2588 5.1 %RANDOM
Rwork0.18664 ---
all0.188 50931 --
obs0.18799 48343 95.14 %-
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: 23.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→25.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 39 608 6988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226479
X-RAY DIFFRACTIONr_bond_other_d0.0020.026116
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9728768
X-RAY DIFFRACTIONr_angle_other_deg0.735314235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3445834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021180
X-RAY DIFFRACTIONr_nbd_refined0.1830.21361
X-RAY DIFFRACTIONr_nbd_other0.2150.27354
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0770.23967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2423
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.54161
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83626704
X-RAY DIFFRACTIONr_scbond_it0.94232318
X-RAY DIFFRACTIONr_scangle_it1.6694.52064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 169
Rwork0.228 3300
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)
10.31880.0314-0.11550.2522-0.06240.5229-0.003-0.0121-0.0319-0.03640.03420.00950.09710.0495-0.03110.0460.0197-0.01130.01910.00810.042223.81610.971817.4841
20.4483-0.1686-0.11530.2722-0.1350.7839-0.0297-0.12270.00740.10.08180.0502-0.05880.0859-0.05210.05070.03960.01170.07210.00760.012518.866420.264448.7929
30.19470.03520.11410.46170.12640.3371-0.01090.0089-0.0052-0.03590.04320.0032-0.06190.026-0.03230.0357-0.00560.00070.029-0.00620.034520.027737.966615.1739
40.0694-0.0319-0.00620.346-0.03920.2987-0.0154-0.0259-0.0044-0.00060.04310.0125-0.00290.0163-0.02770.0020.0064-0.0030.02920.00740.03819.503420.317125.4128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 2853 - 285
2X-RAY DIFFRACTION2BB3 - 2853 - 285
3X-RAY DIFFRACTION3CC3 - 2853 - 285
4X-RAY DIFFRACTION4AM707 - 925

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