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- PDB-2v0p: The Structure of Tap42 Alpha4 Subunit -

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Basic information

Entry
Database: PDB / ID: 2v0p
TitleThe Structure of Tap42 Alpha4 Subunit
ComponentsTYPE 2A PHOSPHATASE-ASSOCIATED PROTEIN 42
KeywordsHYDROLASE INHIBITOR / PHOSPHORYLATION / SIGNAL TRANSDUCTION INHIBITOR
Function / homology
Function and homology information


regulation of dephosphorylation / extrinsic component of membrane / positive regulation of transcription by RNA polymerase I / TOR signaling / negative regulation of signal transduction / protein phosphatase 2A binding / cytosol
Similarity search - Function
TAP42-like family / TAP46-like protein / TAP42/TAP46-like superfamily / TAP42-like family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Type 2A phosphatase-associated protein 42
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsRoe, S.M. / Yang, J. / Barford, D.
CitationJournal: Biochemistry / Year: 2007
Title: The Structure of Tap42/Alpha4 Reveals a Tetratricopeptide Repeat-Like Fold and Provides Insights Into Pp2A Regulation.
Authors: Yang, J. / Roe, S.M. / Prickett, T.D. / Brautigan, D.L. / Barford, D.
History
DepositionMay 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE 2A PHOSPHATASE-ASSOCIATED PROTEIN 42
B: TYPE 2A PHOSPHATASE-ASSOCIATED PROTEIN 42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3956
Polymers55,1342
Non-polymers2624
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.633, 48.308, 71.960
Angle α, β, γ (deg.)81.31, 87.94, 69.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TYPE 2A PHOSPHATASE-ASSOCIATED PROTEIN 42 / TAP42


Mass: 27566.816 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-234
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): B834 / References: UniProt: Q04372
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: THE PROTEIN WAS CONCENTRATED TO 10 MG/ML BEFORE CRYSTALLIZATION. CRYSTALS WERE GROWN AT 20C USING THE HANGING DROP METHOD. ONE MICROLITRE OF PROTEIN WAS MIXED WITH AN EQUAL VOLUME OF ...Details: THE PROTEIN WAS CONCENTRATED TO 10 MG/ML BEFORE CRYSTALLIZATION. CRYSTALS WERE GROWN AT 20C USING THE HANGING DROP METHOD. ONE MICROLITRE OF PROTEIN WAS MIXED WITH AN EQUAL VOLUME OF CRYSTALLIZATION BUFFER: 20% (W/V) PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M MAGNESIUM ACETATE AND 2MM DTT. CRYSTALS WERE OPTIMISED BY SEEDING.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9775
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 49867 / % possible obs: 96.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.6 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→71.07 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.611 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2458 5.19 %RANDOM
Rwork0.238 ---
obs0.239 48202 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.804 Å2-0.632 Å2-1.751 Å2
2---0.147 Å21.419 Å2
3----0.525 Å2
Refinement stepCycle: LAST / Resolution: 1.8→71.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 4 253 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223611
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9914857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36725.281178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98115729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3811519
X-RAY DIFFRACTIONr_chiral_restr0.1170.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022623
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21865
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22549
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3261.52232
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93623495
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.53831519
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7724.51359
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: 8.01→71.07 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.198 14
Rwork0.231 574
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)
11.86130.57360.8022.1921-0.41192.3515-0.0676-0.00010.0733-0.0140.04890.0165-0.1147-0.02830.0188-0.22130.02290.0498-0.2046-0.008-0.232743.16744.8627.122
20.54590.51540.50153.1339-1.21491.53740.0202-0.05560.05180.2945-0.0883-0.0974-0.16590.1020.0681-0.0718-0.0192-0.0546-0.04660.0158-0.09327.5663.243-4.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 234
2X-RAY DIFFRACTION2B2 - 234

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