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- PDB-3iom: Crystal structure of Purine Nucleoside Phosphorylase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 3iom
TitleCrystal structure of Purine Nucleoside Phosphorylase from Mycobacterium tuberculosis in complex with 2'-Deoxyguanosine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase / Mycobacterium tuberculosis / 2 -deoxyguanosine / Glycosyltransferase
Function / homology
Function and homology information


deoxyguanosine catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
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 / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXY-GUANOSINE / Purine nucleoside phosphorylase / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
Authorsde Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Crystallographic and docking studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis.
Authors: Ducati, R.G. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9266
Polymers55,1992
Non-polymers7274
Water3,765209
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8889
Polymers82,7983
Non-polymers1,0906
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7560 Å2
ΔGint-109 kcal/mol
Surface area25540 Å2
MethodPISA
2
B: Purine nucleoside phosphorylase
hetero molecules

B: Purine nucleoside phosphorylase
hetero molecules

B: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8889
Polymers82,7983
Non-polymers1,0906
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7600 Å2
ΔGint-95 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.480, 113.480, 85.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Details2

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Components

#1: Protein Purine nucleoside phosphorylase / PNP / Inosine phosphorylase


Mass: 27599.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Mycobacterium tuberculosis
Gene: deoD, MT3406, MTV016.06, punA, punA (deoD) (Rv3307) (MT3406) (MTV016.06), Rv3307
Production host: Escherichia coli (E. coli)
References: UniProt: P0A538, UniProt: P9WP01*PLUS, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 1.91 Å3/Da / Density % sol: 35.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: The protein was cocrystallized with a 1:0.5:1 stoichiometry of 500 mM Na2SO4 (Merck) and 3 mM 2dGuo (Fluka Biochemika), respectively, by hanging-drop vapor diffusion at 18 C. MtPNP protein ...Details: The protein was cocrystallized with a 1:0.5:1 stoichiometry of 500 mM Na2SO4 (Merck) and 3 mM 2dGuo (Fluka Biochemika), respectively, by hanging-drop vapor diffusion at 18 C. MtPNP protein (1 L of 25 mg mL-1 in 50 mM tris(hydroxymethyl)aminomethane (Tris) pH 7.6) had been previously mixed with an equal volume of the reservoir solution containing 100 mM Tris pH 8.0, 25% poly(ethylene glycol) (PEG) 3350, and 25 mM MgCl2 and hanging drops (3.5 L) were equilibrated against 400 L of the reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.428 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.428 Å / Relative weight: 1
ReflectionResolution: 2.14→28.69 Å / Num. all: 22411 / Num. obs: 22163 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 21.642 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 5.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 3.5 / Num. unique all: 625 / Rsym value: 0.138 / % possible all: 81.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G2O

1g2o


Resolution: 2.14→28.34 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.352 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24894 1134 5.1 %RANDOM
Rwork0.17545 ---
all0.1792 22163 --
obs0.1792 21023 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.181 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.14→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 48 209 4049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213914
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9925362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2055522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7522.74146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8741534
X-RAY DIFFRACTIONr_chiral_restr0.1180.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022984
X-RAY DIFFRACTIONr_nbd_refined0.2520.22228
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.2146
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.221
X-RAY DIFFRACTIONr_mcbond_it1.0231.52598
X-RAY DIFFRACTIONr_mcangle_it1.7824132
X-RAY DIFFRACTIONr_scbond_it2.90431316
X-RAY DIFFRACTIONr_scangle_it4.5634.51230
LS refinement shellResolution: 2.143→2.198 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 81 -
Rwork0.169 1406 -
obs--90.62 %

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