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- PDB-2hv7: Crystal structure of phosphotyrosyl phosphatase activator bound t... -

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Basic information

Entry
Database: PDB / ID: 2hv7
TitleCrystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS
ComponentsProtein phosphatase 2A, regulatory subunit B
KeywordsUNKNOWN FUNCTION / phosphotyrosyl phosphatase activator / PP2A / phosphatase / 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 / negative regulation of phosphoprotein phosphatase activity / ATPase complex / 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 / negative regulation of phosphoprotein phosphatase activity / ATPase complex / 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
ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein phosphatase 2A activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChao, Y. / Jeffrey, J.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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

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Assembly

Deposited unit
A: Protein phosphatase 2A, regulatory subunit B
B: Protein phosphatase 2A, regulatory subunit B
C: Protein phosphatase 2A, regulatory subunit B
D: Protein phosphatase 2A, regulatory subunit B
E: Protein phosphatase 2A, regulatory subunit B
F: Protein phosphatase 2A, regulatory subunit B
G: Protein phosphatase 2A, regulatory subunit B
H: Protein phosphatase 2A, regulatory subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,26212
Polymers294,5538
Non-polymers1,7094
Water0
1
A: Protein phosphatase 2A, regulatory subunit B


Theoretical massNumber of molelcules
Total (without water)36,8191
Polymers36,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein phosphatase 2A, regulatory subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2462
Polymers36,8191
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein phosphatase 2A, regulatory subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2462
Polymers36,8191
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein phosphatase 2A, regulatory subunit B


Theoretical massNumber of molelcules
Total (without water)36,8191
Polymers36,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein phosphatase 2A, regulatory subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2462
Polymers36,8191
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protein phosphatase 2A, regulatory subunit B


Theoretical massNumber of molelcules
Total (without water)36,8191
Polymers36,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Protein phosphatase 2A, regulatory subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2462
Polymers36,8191
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Protein phosphatase 2A, regulatory subunit B


Theoretical massNumber of molelcules
Total (without water)36,8191
Polymers36,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.041, 86.096, 95.099
Angle α, β, γ (deg.)73.91, 89.97, 73.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31F
41H
12B
22C
32E
42G
13B
23C
33E
43G

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSERAA22 - 32222 - 322
21ASNASNSERSERDD22 - 32222 - 322
31ASNASNSERSERFF22 - 32222 - 322
41ASNASNSERSERHH22 - 32222 - 322
12ASNASNSERSERBB22 - 32222 - 322
22ASNASNSERSERCC22 - 32222 - 322
32ASNASNSERSEREE22 - 32222 - 322
42ASNASNSERSERGG22 - 32222 - 322
13ADPADPADPADPBI324
23ADPADPADPADPCJ324
33ADPADPADPADPEK324
43ADPADPADPADPGL324

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 36819.117 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15257
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 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: 2.5→100 Å / Num. all: 80608 / Num. obs: 76255 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rsym value: 0.083
Reflection shellResolution: 2.5→2.6 Å / Rsym value: 0.377 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2HV6

2hv6


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.88 / SU B: 39.352 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31246 3608 5.1 %RANDOM
Rwork0.2486 ---
all0.25 76416 --
obs0.25183 67017 87.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.367 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å2-0.83 Å20.24 Å2
2---2.78 Å21.34 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19504 0 108 0 19612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02220172
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.95527404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7752400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57223.966928
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.404153416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8511596
X-RAY DIFFRACTIONr_chiral_restr0.0930.22968
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215292
X-RAY DIFFRACTIONr_nbd_refined0.2210.29839
X-RAY DIFFRACTIONr_nbtor_refined0.3070.213971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2597
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.2193
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.219
X-RAY DIFFRACTIONr_mcbond_it0.4331.512291
X-RAY DIFFRACTIONr_mcangle_it0.722219536
X-RAY DIFFRACTIONr_scbond_it1.0539040
X-RAY DIFFRACTIONr_scangle_it1.6314.57868
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1204medium positional0.170.5
12D1204medium positional0.240.5
13F1204medium positional0.180.5
14H1204medium positional0.20.5
21B1204medium positional0.20.5
22C1204medium positional0.240.5
23E1204medium positional0.20.5
24G1204medium positional0.170.5
11A1235loose positional0.415
12D1235loose positional0.435
13F1235loose positional0.365
14H1235loose positional0.415
21B1235loose positional0.415
22C1235loose positional0.515
23E1235loose positional0.415
24G1235loose positional0.385
31B27loose positional0.355
32C27loose positional0.555
33E27loose positional0.545
34G27loose positional0.435
11A1204medium thermal0.432
12D1204medium thermal0.342
13F1204medium thermal0.372
14H1204medium thermal0.392
21B1204medium thermal0.382
22C1204medium thermal0.392
23E1204medium thermal0.322
24G1204medium thermal0.322
11A1235loose thermal1.1810
12D1235loose thermal1.0310
13F1235loose thermal1.1210
14H1235loose thermal1.1410
21B1235loose thermal1.2210
22C1235loose thermal1.1810
23E1235loose thermal0.9610
24G1235loose thermal0.9710
31B27loose thermal14.5510
32C27loose thermal5.4310
33E27loose thermal7.4510
34G27loose thermal12.3410
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 243 -
Rwork0.335 4084 -
obs--73.15 %

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