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- PDB-2ixn: CRYSTAL STRUCTURE OF THE PP2A PHOSPHATASE ACTIVATOR Ypa2 PTPA2 -

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Basic information

Entry
Database: PDB / ID: 2ixn
TitleCRYSTAL STRUCTURE OF THE PP2A PHOSPHATASE ACTIVATOR Ypa2 PTPA2
ComponentsSERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 2
KeywordsISOMERASE / PP2A PHOSPHATASE ACTIVATOR PROLYL ISOMERASE PTPA
Function / homology
Function and homology information


protein tyrosine phosphatase activator activity / protein phosphatase type 2A complex / protein phosphatase regulator activity / response to osmotic stress / mitotic spindle organization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleus / cytoplasm
Similarity search - Function
Phosphotyrosyl phosphate activator, C-terminal lid domain / Phosphotyrosyl phosphatase activator, PTPA / PTPA superfamily / Phosphotyrosyl phosphatase activator, C-terminal lid domain / Phosphotyrosyl phosphate activator (PTPA) protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A activator 2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLeulliot, N. / Vicentini, G. / Jordens, J. / Quevillon-Cheruel, S. / Schiltz, M. / Barford, D. / Van Tilbeurgh, H. / Goris, J.
CitationJournal: Mol.Cell / Year: 2006
Title: Crystal Structure of the Pp2A Phosphatase Activator: Implications for its Pp2A-Specific Ppiase Activity
Authors: Leulliot, N. / Vicentini, G. / Jordens, J. / Quevillon-Cheruel, S. / Schiltz, M. / Barford, D. / Van Tilbeurgh, H. / Goris, J.
History
DepositionJul 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 2
B: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 2


Theoretical massNumber of molelcules
Total (without water)72,6812
Polymers72,6812
Non-polymers00
Water00
1
A: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 2


Theoretical massNumber of molelcules
Total (without water)36,3411
Polymers36,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 2


Theoretical massNumber of molelcules
Total (without water)36,3411
Polymers36,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)157.930, 171.042, 53.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 2 / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PTPA-2 / PPIASE PTPA-2 / ROTAMASE PTPA-2 / PTPA2 / ...PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PTPA-2 / PPIASE PTPA-2 / ROTAMASE PTPA-2 / PTPA2 / PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR 2


Mass: 36340.621 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD (DE3) / References: UniProt: Q12461

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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: 2.7 Å3/Da / Density % sol: 54.16 %
Crystal growpH: 5.6
Details: 16% PEG4000, 0.4M KCL, PH 5.6, 0.1M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 176445 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.87 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
HYSSphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 36.688 / SU ML: 0.323 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 897 5.2 %RANDOM
Rwork0.199 ---
obs0.202 16283 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2--2.13 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 0 0 4792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224920
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2261.9546628
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6785572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58223.675234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.9515902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7921524
X-RAY DIFFRACTIONr_chiral_restr0.160.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023674
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.280.22453
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.23362
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3260.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7511.52939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36924660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12932264
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3384.51968
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 64
Rwork0.312 1201
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.44371.784-0.22081.8848-0.44972.08190.196-0.6641-0.08370.0696-0.00680.12780.092-0.18-0.18910.0885-0.0627-0.0650.40110.07780.069856.96428.2261.091
22.25230.78680.72462.463-0.99885.063-0.17080.2932-0.0674-0.0491-0.17920.0224-0.32810.27220.350.0034-0.04370.01450.35540.06290.021220.55116.704-22.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 299
2X-RAY DIFFRACTION2B3 - 299

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