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- PDB-2isc: Crystal structure of Purine Nucleoside Phosphorylase from Trichom... -

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Basic information

Entry
Database: PDB / ID: 2isc
TitleCrystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A
Componentspurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-223 / PHOSPHATE ION / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRinaldo-Matthis, A. / Almo, S.C. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2007
Title: Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues
Authors: Rinaldo-Matthis, A. / Wing, C. / Ghanem, M. / Deng, H. / Wu, P. / Gupta, A. / Tyler, P.C. / Evans, G.B. / Furneaux, R.H. / Almo, S.C. / Wang, C.C. / Schramm, V.L.
History
DepositionOct 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 21, 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

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Assembly

Deposited unit
A: purine nucleoside phosphorylase
B: purine nucleoside phosphorylase
C: purine nucleoside phosphorylase
D: purine nucleoside phosphorylase
E: purine nucleoside phosphorylase
F: purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,53720
Polymers158,1976
Non-polymers2,34014
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25880 Å2
ΔGint-166 kcal/mol
Surface area44460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.402, 113.821, 195.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains the functional hexameric unit

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Components

#1: Protein
purine nucleoside phosphorylase / E.C.2.4.2.1 / PNP


Mass: 26366.246 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: A2E7Y6, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-223 / (3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL / 4'-DEAZA-1'-AZA-2'-DEOXY-1'-(9-METHYLENE)-IMMUCILLIN-A


Mass: 263.296 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H17N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M Sodium Acetate, 25.5% PEG 4000, 0.085 M TrisHCL, 15% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979099 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2006
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979099 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 51179 / Num. obs: 50207 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 50.856 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.116 / Χ2: 0.597 / Net I/σ(I): 5.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.72 / Num. unique all: 4713 / Rsym value: 0.594 / Χ2: 0.561 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.99 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.382 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2549 5.1 %RANDOM
Rwork0.199 ---
all0.20187 51139 --
obs0.202 50106 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10721 0 154 160 11035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211106
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.96915043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30651385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41424.267464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.991151863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6271547
X-RAY DIFFRACTIONr_chiral_restr0.0920.21711
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028283
X-RAY DIFFRACTIONr_nbd_refined0.2170.25635
X-RAY DIFFRACTIONr_nbtor_refined0.3110.27637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2496
X-RAY DIFFRACTIONr_metal_ion_refined0.4050.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0690.23
X-RAY DIFFRACTIONr_mcbond_it0.6351.57095
X-RAY DIFFRACTIONr_mcangle_it1.14211139
X-RAY DIFFRACTIONr_scbond_it1.26834497
X-RAY DIFFRACTIONr_scangle_it2.0314.53904
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 175 -
Rwork0.271 3248 -
obs-3423 92.71 %

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