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- PDB-1z39: Crystal structure of Trichomonas vaginalis purine nucleoside phos... -

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Basic information

Entry
Database: PDB / ID: 1z39
TitleCrystal structure of Trichomonas vaginalis purine nucleoside phosphorylase complexed with 2'-deoxyinosine
Componentspurine nucleoside phosphorylase
KeywordsTRANSFERASE / alpha-beta-alpha sandwich
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 2'-DEOXYINOSINE
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, Y. / Wang, W.H. / Wu, S.W. / Wang, C.C. / Ealick, S.E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Identification of a subversive substrate of Trichomonas vaginalis purine nucleoside phosphorylase and the crystal structure of the enzyme-substrate complex.
Authors: Zang, Y. / Wang, W.H. / Wu, S.W. / Ealick, S.E. / Wang, C.C.
History
DepositionMar 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_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
Remark 999 Sequence There is currently no match for the protein sequence in the standard databases

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0662
Polymers25,8141
Non-polymers2521
Water1,00956
1
A: purine nucleoside phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,39512
Polymers154,8826
Non-polymers1,5136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area23620 Å2
ΔGint-117 kcal/mol
Surface area44780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)136.800, 136.800, 136.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-302-

HOH

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Components

#1: Protein purine nucleoside phosphorylase


Mass: 25813.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Production host: Escherichia coli (E. coli) / Keywords: purine nucleoside phosphorylase / References: purine-nucleoside phosphorylase
#2: Chemical ChemComp-2ND / 2'-DEOXYINOSINE


Mass: 252.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 4.3 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG400, ethylene glycol, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9766 / Wavelength: 0.9766 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.6→43.26 Å / Num. all: 14030 / Num. obs: 13005 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23 Å2
Reflection shellResolution: 2.6→2.76 Å / % possible all: 85

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PKE

1pke


Resolution: 2.6→43.26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 138860.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 634 4.9 %RANDOM
Rwork0.205 ---
all0.205 14030 --
obs0.205 13005 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5669 Å2 / ksol: 0.375963 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 18 56 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 92 4.8 %
Rwork0.223 1831 -
obs-1831 85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION22ND.PARAM2ND.TOP
X-RAY DIFFRACTION3WATER.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMWATER.TOP

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