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- PDB-1td1: Crystal Structure of the Purine Nucleoside Phosphorylase from Sch... -

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Basic information

Entry
Database: PDB / ID: 1td1
TitleCrystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with acetate
Componentspurine-nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase
Function / homology
Function and homology information


nucleoside metabolic process / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
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 / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / Refinement description / 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)93,7696
Polymers93,5923
Non-polymers1773
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-59 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.231, 120.212, 131.933
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


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 40.6 %
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: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2002 / Details: Si 111
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→54 Å / Num. all: 61501 / Num. obs: 58392 / % possible obs: 93.5 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.063
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.31 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SmPNP refined at 2.1 angstrons

Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.516 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.3 / σ(I): 2.3 / ESU R: 0.174 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21011 3109 5.1 %RANDOM
Rwork0.1871 ---
all0.18875 61501 --
obs0.1875 58392 93.5 %-
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: 22.692 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å20 Å2
2---0.73 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6342 0 12 580 6934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226459
X-RAY DIFFRACTIONr_bond_other_d0.0020.026099
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.9698742
X-RAY DIFFRACTIONr_angle_other_deg0.738314201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3655834
X-RAY DIFFRACTIONr_chiral_restr0.0630.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027144
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
X-RAY DIFFRACTIONr_nbd_refined0.1860.21366
X-RAY DIFFRACTIONr_nbd_other0.2170.27396
X-RAY DIFFRACTIONr_nbtor_other0.0780.23988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2445
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.225
X-RAY DIFFRACTIONr_mcbond_it0.5011.54158
X-RAY DIFFRACTIONr_mcangle_it0.93526696
X-RAY DIFFRACTIONr_scbond_it1.14232301
X-RAY DIFFRACTIONr_scangle_it2.0074.52046
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 211
Rwork0.266 3825
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)
10.26720.0977-0.1460.3868-0.15030.48560.0139-0.0165-0.0243-0.06260.03770.01080.10960.0543-0.05150.07030.0288-0.0230.0566-0.00720.067223.93450.8717.6116
20.3571-0.16470.15140.4639-0.15570.7383-0.0018-0.0599-0.00120.14890.0480.0375-0.0730.0325-0.04630.08720.02420.02040.0840.01420.03619.060220.27848.8486
30.25210.12790.20820.58640.11020.3808-0.02690.0042-0.024-0.05580.05470.0245-0.07910.042-0.02780.0577-0.0043-0.00380.0608-0.01080.054820.094337.832315.1691
4-0.01120.01880.06270.4273-0.06520.3423-0.0063-0.0218-0.016-0.01540.03710.04360.00460.0348-0.03080.00330.0137-0.0010.05930.01010.060319.396420.052525.4282
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 285
2X-RAY DIFFRACTION2B3 - 285
3X-RAY DIFFRACTION3C3 - 285
4X-RAY DIFFRACTION4A701 - 906
5X-RAY DIFFRACTION4C703 - 923
6X-RAY DIFFRACTION4B702 - 854

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