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- PDB-3ix2: CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBAC... -

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Basic information

Entry
Database: PDB / ID: 3ix2
TitleCRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ACYCLOVIR
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Mycobacterium tuberculosis / Purine Nucleoside Phosphorylase / Acyclovir
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Putative purine nucleotide phosphorylase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
9-HYROXYETHOXYMETHYLGUANINE / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis variant bovis AF2122/97 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S.
CitationJournal: Biochimie / Year: 2012
Title: Crystal structure and molecular dynamics studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis associated with acyclovir.
Authors: Caceres, R.A. / Timmers, L.F. / Ducati, R.G. / da Silva, D.O. / Basso, L.A. / de Azevedo Jr., W.F. / Santos, D.S.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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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)83,7599
Polymers82,7983
Non-polymers9616
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-64 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.177, 135.759, 41.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Purine nucleoside phosphorylase / PNP / Pu-NPase / Inosine phosphorylase / Inosine-guanosine phosphorylase


Mass: 27599.457 Da / Num. of mol.: 3 / Fragment: PURINE NUCLEOSIDE PHOSPHORYLASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis variant bovis AF2122/97 (bacteria)
Strain: ATCC BAA-935 / AF2122/97 / Gene: punA, deoD, BQ2027_MB3335 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A539, 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-AC2 / 9-HYROXYETHOXYMETHYLGUANINE


Mass: 225.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11N5O3 / Comment: medication, antivirus*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 1.79 Å3/Da / Density % sol: 31.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, pH 8.0, 25%PEG 3350, and 25 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR scanner 300 mm plate / Detector: CCD / Date: Feb 2, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.1→33.94 Å / Num. all: 39559 / Num. obs: 35559 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3 / Num. unique all: 2200 / Rsym value: 0.2 / % possible all: 90

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N3I

1n3i


Resolution: 2.1→33.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.369 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26197 1679 5 %RANDOM
Rwork0.18256 ---
all0.18653 35559 --
obs0.18653 31718 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.187 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.03 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 63 388 6139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0215859
X-RAY DIFFRACTIONr_angle_refined_deg2.3881.9898019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1395783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26722.74219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37415834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.61551
X-RAY DIFFRACTIONr_chiral_restr0.2920.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024476
X-RAY DIFFRACTIONr_nbd_refined0.2670.23825
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2629
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.2200
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.222
X-RAY DIFFRACTIONr_mcbond_it1.9461.53897
X-RAY DIFFRACTIONr_mcangle_it2.92326198
X-RAY DIFFRACTIONr_scbond_it3.12431962
X-RAY DIFFRACTIONr_scangle_it4.7224.51821
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 125 -
Rwork0.214 2238 -
obs--91.95 %

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