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Basic information

Entry
Database: PDB / ID: 3scz
TitleCombining crystallographic, thermodynamic, and molecular dynamics studies of Mycobacterium tuberculosis purine nucleoside phosphorylase
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Tuberculosis / Purine nucleoside phosphorylase / Inosine / Hypoxanthine
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
HYPOXANTHINE / Purine nucleoside phosphorylase / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
Authorsde Azevedo Jr., W.F. / Caceres, R.A. / Timmers, L.F.S.M. / Ducati, R.G. / Rosado, L.A. / Basso, L.A. / Santos, D.S.
CitationJournal: To be Published
Title: Combining crystallographic, thermodynamic, and molecular dynamics studies of Mycobacterium tuberculosis purine nucleoside phosphorylase
Authors: de Azevedo Jr., W.F.
History
DepositionJun 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4714
Polymers55,1992
Non-polymers2722
Water5,080282
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)83,2076
Polymers82,7983
Non-polymers4083
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 area6470 Å2
ΔGint-35 kcal/mol
Surface area27060 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)83,2076
Polymers82,7983
Non-polymers4083
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 area6550 Å2
ΔGint-35 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.590, 115.590, 86.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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) / Gene: punA, deoD, Rv3307, MT3406, MTV016.06 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A538, UniProt: P9WP01*PLUS, purine-nucleoside phosphorylase
#2: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MtPNP:INO:SO4 and MtPNP:HX were crystallized using the experimental conditions described elsewhere. PNP solution was concentrated to 25 mg/mL and co-crystallized with INO:SO4 and HX. Hanging ...Details: MtPNP:INO:SO4 and MtPNP:HX were crystallized using the experimental conditions described elsewhere. PNP solution was concentrated to 25 mg/mL and co-crystallized with INO:SO4 and HX. Hanging drops were prepared mixing 1 uL of protein solution and 1 uL of reservoir solution (100 mM Tris, pH 8.0, 25 % PEG3350, 25 mM MgCl2), 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: 1.431 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 2, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 1.95→21.09 Å / Num. obs: 31352 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.95-21100
2-2.751100
2.76-3.071100
3.08-3.551100
3.56-4.351100
4.36-6.161100
6.17-28.897199.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→21.09 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22767 1578 5 %RANDOM
Rwork0.17368 ---
obs0.17635 29751 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.071 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→21.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 20 282 4101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213894
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9835329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07522.74146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74215556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6441534
X-RAY DIFFRACTIONr_chiral_restr0.1340.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212982
X-RAY DIFFRACTIONr_mcbond_it0.9571.52604
X-RAY DIFFRACTIONr_mcangle_it1.61124142
X-RAY DIFFRACTIONr_scbond_it2.64431290
X-RAY DIFFRACTIONr_scangle_it4.0434.51187
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 111 -
Rwork0.187 2206 -
obs--100 %

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