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- PDB-1g2o: CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBAC... -

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Basic information

Entry
Database: PDB / ID: 1g2o
TitleCRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A TRANSITION-STATE INHIBITOR
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsTRANSFERASE / trimer / transition-state complex
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
Chem-IMH / PHOSPHATE ION / Purine nucleoside phosphorylase / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsShi, W. / Basso, L.A. / Tyler, P.C. / Furneaux, R.H. / Blanchard, J.S. / Almo, S.C. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2001
Title: Structures of purine nucleoside phosphorylase from Mycobacterium tuberculosis in complexes with immucillin-H and its pieces.
Authors: Shi, W. / Basso, L.A. / Santos, D.S. / Tyler, P.C. / Furneaux, R.H. / Blanchard, J.S. / Almo, S.C. / Schramm, V.L.
History
DepositionOct 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 5, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / reflns / struct_site
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.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns.number_all / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 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:
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)83,8829
Polymers82,7983
Non-polymers1,0846
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-73 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.625, 102.625, 128.478
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a trimer in the asymmetric unit.

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Components

#1: Protein PURINE NUCLEOSIDE PHOSPHORYLASE


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: P9WP01*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-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


Mass: 266.253 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H14N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Magnesium chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
25 mMsodium phosphate1drop
3100 mMTris1reservoirpH8.0
425 %PEG40001reservoir
525 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 78938 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 35.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 8.3 / Num. unique all: 7823 / Rsym value: 0.217 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 513786 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.217

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3X

1c3x


Resolution: 1.75→20 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 7608 10 %random
Rwork0.189 ---
obs0.191 75787 95.6 %-
all-77969 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8392 Å2 / ksol: 0.392985 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-0.55 Å20 Å2
2---1.62 Å20 Å2
3---3.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 72 485 6245
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it0.61.5
X-RAY DIFFRACTIONc_mcangle_it0.992
X-RAY DIFFRACTIONc_scbond_it1.052
X-RAY DIFFRACTIONc_scangle_it1.612.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 1095 10 %
Rwork0.193 10575 -
obs-10575 89 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.191 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.226 / % reflection Rfree: 10 % / Rfactor Rwork: 0.193

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