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- PDB-1jdu: CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE -

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Basic information

Entry
Database: PDB / ID: 1jdu
TitleCRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE
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
Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)77,2903
Polymers77,2903
Non-polymers00
Water3,189177
1
A: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
B: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
C: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE

A: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
B: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
C: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE


Theoretical massNumber of molelcules
Total (without water)154,5816
Polymers154,5816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area16380 Å2
ΔGint-86 kcal/mol
Surface area49950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.6, 175.5, 87.4
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Detailshexamer generated from the trimer in the asymmetric unit by the crystallographic two fold

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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.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 51.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: dioxane, MPD, MgCl2, NaCl, Tris.HCl at pH 7.4, VAPOR DIFFUSION, HANGING DROP, 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: NSLS / Beamline: X12C / Wavelength: 1.023 Å
DetectorType: BRANDEIS / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.023 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 27294 / Num. obs: 27294 / % possible obs: 95.5 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.8
Reflection shellHighest resolution: 2.5 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.5 / % possible all: 87.4
Reflection
*PLUS
Num. measured all: 73267
Reflection shell
*PLUS
% possible obs: 87.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ECP

1ecp


Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1149 5 %RANDOM
Rwork0.184 ---
all-24579 --
obs-23534 --
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 0 177 5517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.225
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.2 Å2

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