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- PDB-2hv6: Crystal structure of the phosphotyrosyl phosphatase activator -

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Basic information

Entry
Database: PDB / ID: 2hv6
TitleCrystal structure of the phosphotyrosyl phosphatase activator
ComponentsProtein phosphatase 2A, regulatory subunit B
KeywordsUNKNOWN FUNCTION / phosphotyrosyl phosphatase activator / phosphatase / PP2A / phosphatase specificity
Function / homology
Function and homology information


protein tyrosine phosphatase activator activity / negative regulation of protein dephosphorylation / regulation of phosphoprotein phosphatase activity / protein phosphatase type 2A complex / protein phosphatase regulator activity / ATPase complex / negative regulation of phosphoprotein phosphatase activity / positive regulation of phosphoprotein phosphatase activity / positive regulation of protein dephosphorylation / calcium channel complex ...protein tyrosine phosphatase activator activity / negative regulation of protein dephosphorylation / regulation of phosphoprotein phosphatase activity / protein phosphatase type 2A complex / protein phosphatase regulator activity / ATPase complex / negative regulation of phosphoprotein phosphatase activity / positive regulation of phosphoprotein phosphatase activity / positive regulation of protein dephosphorylation / calcium channel complex / mitotic spindle organization / protein phosphatase 2A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of apoptotic process / signaling receptor binding / protein homodimerization activity / extracellular exosome / nucleoplasm / ATP binding / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChao, Y. / Jeffrey, P.D. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2006
Title: Structure and mechanism of the phosphotyrosyl phosphatase activator.
Authors: Chao, Y. / Xing, Y. / Chen, Y. / Xu, Y. / Lin, Z. / Li, Z. / Jeffrey, P.D. / Stock, J.B. / Shi, Y.
History
DepositionJul 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Protein phosphatase 2A, regulatory subunit B
B: Protein phosphatase 2A, regulatory subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6633
Polymers73,6382
Non-polymers241
Water3,693205
1
A: Protein phosphatase 2A, regulatory subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8432
Polymers36,8191
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein phosphatase 2A, regulatory subunit B


Theoretical massNumber of molelcules
Total (without water)36,8191
Polymers36,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.250, 42.790, 75.570
Angle α, β, γ (deg.)90.00, 108.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein phosphatase 2A, regulatory subunit B / PR 53


Mass: 36819.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R4 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15257
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2mM Mg Formate, 5% glycerol, 17.5% PEG3350 (w/v), 0.1 M Bistris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. all: 38601 / Num. obs: 36825 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.056
Reflection shellResolution: 1.9→2 Å / Rsym value: 0.313 / % possible all: 94.6

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Processing

Software
NameClassification
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2G62

2g62


Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1726 -random
Rwork0.183 ---
all0.19 38209 --
obs0.19 35226 92.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 1 205 5038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.37

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