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- PDB-2a8y: Crystal structure of 5'-deoxy-5'methylthioadenosine phosphorylase... -

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Basic information

Entry
Database: PDB / ID: 2a8y
TitleCrystal structure of 5'-deoxy-5'methylthioadenosine phosphorylase complexed with 5'-deoxy-5'methylthioadenosine and sulfate
Components5'-methylthioadenosine phosphorylase (mtaP)
KeywordsTRANSFERASE / alpha/beta / beta sheet / beta barrel
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsZhang, Y. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus, a thermophilic enzyme stabilized by intramolecular disulfide bonds.
Authors: Zhang, Y. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E.
History
DepositionJul 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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: 5'-methylthioadenosine phosphorylase (mtaP)
B: 5'-methylthioadenosine phosphorylase (mtaP)
C: 5'-methylthioadenosine phosphorylase (mtaP)
D: 5'-methylthioadenosine phosphorylase (mtaP)
E: 5'-methylthioadenosine phosphorylase (mtaP)
F: 5'-methylthioadenosine phosphorylase (mtaP)
G: 5'-methylthioadenosine phosphorylase (mtaP)
H: 5'-methylthioadenosine phosphorylase (mtaP)
I: 5'-methylthioadenosine phosphorylase (mtaP)
J: 5'-methylthioadenosine phosphorylase (mtaP)
K: 5'-methylthioadenosine phosphorylase (mtaP)
L: 5'-methylthioadenosine phosphorylase (mtaP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,00748
Polymers362,13412
Non-polymers5,87436
Water61,3413405
1
A: 5'-methylthioadenosine phosphorylase (mtaP)
B: 5'-methylthioadenosine phosphorylase (mtaP)
C: 5'-methylthioadenosine phosphorylase (mtaP)
J: 5'-methylthioadenosine phosphorylase (mtaP)
K: 5'-methylthioadenosine phosphorylase (mtaP)
L: 5'-methylthioadenosine phosphorylase (mtaP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,00424
Polymers181,0676
Non-polymers2,93718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29640 Å2
ΔGint-390 kcal/mol
Surface area47440 Å2
MethodPISA
2
D: 5'-methylthioadenosine phosphorylase (mtaP)
E: 5'-methylthioadenosine phosphorylase (mtaP)
F: 5'-methylthioadenosine phosphorylase (mtaP)
G: 5'-methylthioadenosine phosphorylase (mtaP)
H: 5'-methylthioadenosine phosphorylase (mtaP)
I: 5'-methylthioadenosine phosphorylase (mtaP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,00424
Polymers181,0676
Non-polymers2,93718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29220 Å2
ΔGint-364 kcal/mol
Surface area47310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.597, 96.556, 96.628
Angle α, β, γ (deg.)91.57, 91.23, 91.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
5'-methylthioadenosine phosphorylase (mtaP)


Mass: 30177.795 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SsMTAPII / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q97W94, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3405 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→500 Å / Num. all: 579262 / Num. obs: 579262 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 13.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 1 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 55440 / Rsym value: 0.245 / % possible all: 90.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CG6

1cg6


Resolution: 1.45→48.27 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 1148613.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 37861 6.9 %RANDOM
Rwork0.182 ---
all0.183 549659 --
obs0.182 549659 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0119 Å2 / ksol: 0.362326 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-1.21 Å2-0.31 Å2
2---0.45 Å2-0.19 Å2
3---0.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25565 0 360 3405 29330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.21
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 4038 5.1 %
Rwork0.23 75917 -
obs--77.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3mta_param.txtmta_top.txt
X-RAY DIFFRACTION5ion.paramion.top

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