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- PDB-1jpv: Crystal Structure of 5'-deoxy-5'-methylthioadenosine phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 1jpv
TitleCrystal Structure of 5'-deoxy-5'-methylthioadenosine phosphorylase complexed with SO4
Components5'-deoxy-5'-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: 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
DepositionAug 3, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 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
Revision 1.5Oct 30, 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'-deoxy-5'-methylthioadenosine phosphorylase
B: 5'-deoxy-5'-methylthioadenosine phosphorylase
C: 5'-deoxy-5'-methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5796
Polymers77,2903
Non-polymers2883
Water4,612256
1
A: 5'-deoxy-5'-methylthioadenosine phosphorylase
B: 5'-deoxy-5'-methylthioadenosine phosphorylase
C: 5'-deoxy-5'-methylthioadenosine phosphorylase
hetero molecules

A: 5'-deoxy-5'-methylthioadenosine phosphorylase
B: 5'-deoxy-5'-methylthioadenosine phosphorylase
C: 5'-deoxy-5'-methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,15712
Polymers154,5816
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area18030 Å2
ΔGint-215 kcal/mol
Surface area49190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.10, 174.31, 86.97
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

Detailshexamer generated from the trimer in the asymmetric unit by the crystallographic two fold.

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Components

#1: Protein 5'-deoxy-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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: dioxane, MPD, MgCl2, MgSO4, 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: 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: 69926 / Num. obs: 69926 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / % possible all: 92.7
Reflection
*PLUS
Num. obs: 50040 / % possible obs: 95.7 % / Num. measured all: 195119
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 4.4

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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 ssMTAP

Resolution: 1.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3537 5.1 %random
Rwork0.224 ---
all-69880 --
obs-69619 --
Displacement parametersBiso mean: 31.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 15 256 5637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.283
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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