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- PDB-1je1: 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEX WITH GUANOS... -

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Basic information

Entry
Database: PDB / ID: 1je1
Title5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEX WITH GUANOSINE AND SULFATE
Components5'-METHYLTHIOADENOSINE PHOSPHORYLASE
KeywordsTRANSFERASE / alpha-beta protein
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / nucleoside catabolic process / purine-nucleoside phosphorylase / cytosol
Similarity search - Function
Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAppleby, T.C. / Mathews, I.I. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.
Authors: Appleby, T.C. / Mathews, I.I. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Purification and characterization of extremely thermophilic and thermostable 5'-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus. Purine nucleoside phosphorylase ...Title: Purification and characterization of extremely thermophilic and thermostable 5'-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus. Purine nucleoside phosphorylase activity and evidence for intersubunit disulfide bonds
Authors: Cacciapuoti, G. / Porcelli, M. / Bertoldo, C. / De Rosa, M. / Zappia, V.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Three-Dimensional Structure of Human Erythrocytic Purine Nucleoside Phosphorylase At 3.2 Resolution
Authors: Ealick, S.E. / Rule, S.A. / Carter, D.C. / Greenhough, T.J. / Babu, Y.S.
#3: Journal: Structure / Year: 1999
Title: The structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase at 1.7 resolution provides insights into substrate binding and catalysis
Authors: Appleby, T.C. / Erion, M.D. / Ealick, S.E.
History
DepositionJun 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
B: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
C: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
D: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
E: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
F: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,85718
Polymers154,5816
Non-polymers2,27612
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21390 Å2
ΔGint-194 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.8, 87.6, 101.8
Angle α, β, γ (deg.)90.0, 119.99, 90.0
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
5'-METHYLTHIOADENOSINE PHOSPHORYLASE / E.C.2.4.2.28 / MTA PHOSPHORYLASE / MTAP


Mass: 25763.457 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: P50389, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: dioxane, MPD, MgCl2, NaCl, Tris.HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlprotein1drop
228-30 %dioxane1reservoir
312 %MPD1reservoir
40.12 M1reservoirMgCl2
50.04 M1reservoirNaCl
60.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9023 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9023 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 139268 / Num. obs: 139268 / % possible obs: 82 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.4
Reflection shellHighest resolution: 1.8 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.3 / % possible all: 41.7
Reflection
*PLUS
Num. measured all: 543683
Reflection shell
*PLUS
% possible obs: 41.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native complex

Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 6500 5.1 %Random
Rwork0.217 ---
all-127982 --
obs-127814 --
Displacement parametersBiso mean: 28.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10720 0 150 417 11287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.218
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2

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