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- PDB-1n3i: Crystal Structure of Mycobacterium tuberculosis PNP with transiti... -

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Basic information

Entry
Database: PDB / ID: 1n3i
TitleCrystal Structure of Mycobacterium tuberculosis PNP with transition state analog DADMe-ImmH
ComponentsPurine Nucleoside Phosphorylase
KeywordsTRANSFERASE / transition state complex / trimer / PNP
Function / homology
Function and homology information


deoxyguanosine catabolic process / beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / manganese ion binding / magnesium ion binding / ATP binding ...deoxyguanosine catabolic process / beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / manganese ion binding / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Putative purine nucleotide phosphorylase / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily ...Putative purine nucleotide phosphorylase / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / 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-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DIH / PHOSPHATE ION / Purine nucleoside phosphorylase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsLewandowicz, A. / Shi, W. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Basso, L.A. / Santos, D.S. / Almo, S.C. / Schramm, V.L.
CitationJournal: BIOCHEMISTRY / Year: 2003
Title: Over-The-Barrier Transition State Analogues Provide New Chemistries for Inhibitor Design: The Case of Purine Nucleoside Phosphorylase
Authors: Lewandowicz, A. / Shi, W. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Basso, L.A. / Santos, D.S. / Almo, S.C. / Schramm, V.L.
History
DepositionOct 28, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 25, 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
C: Purine Nucleoside Phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8799
Polymers82,7983
Non-polymers1,0816
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-66 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.842, 102.842, 128.763
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is the trimer in the asymmetric unit.

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Components

#1: Protein Purine Nucleoside Phosphorylase / PNP


Mass: 27599.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET-23A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A538, UniProt: P9WIL5*PLUS, 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-DIH / 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one


Mass: 265.288 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H17N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, Magnesium Chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1730000 nMPNP1drop
21.1 mMDADMe-ImmH1drop
33 mMsodium phosphate1droppH8.0
4100 mMTris-HCl1reservoirpH8.0
525 %PEG40001reservoir
625 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2002
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 62570 / Num. obs: 59925 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.036 / Net I/σ(I): 45.9
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 10.3 / Rsym value: 0.105 / % possible all: 76.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 321763 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 76.9 % / Rmerge(I) obs: 0.105

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1G2O

1g2o


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 6018 10 %random
Rwork0.183 ---
obs0.186 59299 94.8 %-
all-59925 --
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.28 Å20 Å2
2---1.19 Å20 Å2
3---2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 72 432 6180
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.218 821 10 %
Rwork0.181 7419 -
obs-7419 80.1 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004724
X-RAY DIFFRACTIONc_angle_deg1.32049
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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