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- PDB-4i5k: PP2A PR70 Holoenzyme model3_diCa_rcsb.pdb bppnat5_extend.mtz -

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Basic information

Entry
Database: PDB / ID: 4i5k
TitlePP2A PR70 Holoenzyme model3_diCa_rcsb.pdb bppnat5_extend.mtz
ComponentsSerine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
KeywordsHYDROLASE / EF Hand / Phosphatase regulatory subunit / PP2A / Cytopasmic
Function / homology
Function and homology information


regulation of cell migration involved in somitogenic axis elongation / eye photoreceptor cell differentiation / somatic muscle development / protein phosphatase type 2A complex / somite development / protein phosphatase regulator activity / regulation of canonical Wnt signaling pathway / somitogenesis / protein dephosphorylation / negative regulation of canonical Wnt signaling pathway ...regulation of cell migration involved in somitogenic axis elongation / eye photoreceptor cell differentiation / somatic muscle development / protein phosphatase type 2A complex / somite development / protein phosphatase regulator activity / regulation of canonical Wnt signaling pathway / somitogenesis / protein dephosphorylation / negative regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / protein-macromolecule adaptor activity / calcium ion binding
Similarity search - Function
Recoverin; domain 1 - #220 / PP2A regulatory subunit B'', EF-hand domain / : / EF-hand domain / P2R3B, EF-hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Recoverin; domain 1 - #220 / PP2A regulatory subunit B'', EF-hand domain / : / EF-hand domain / P2R3B, EF-hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXing, Y. / Jeffrey, P.D. / Shi, Y.
CitationJournal: Cell Res. / Year: 2013
Title: Structure of the Ca(2+)-dependent PP2A heterotrimer and insights into Cdc6 dephosphorylation.
Authors: Wlodarchak, N. / Guo, F. / Satyshur, K.A. / Jiang, L. / Jeffrey, P.D. / Sun, T. / Stanevich, V. / Mumby, M.C. / Xing, Y.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
B: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0876
Polymers67,9272
Non-polymers1604
Water00
1
A: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0443
Polymers33,9631
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0443
Polymers33,9631
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.812, 109.086, 67.651
Angle α, β, γ (deg.)90.00, 109.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha / PP2A subunit B isoform PR72/PR130 / PP2A subunit B isoform R3 isoform / PP2A subunit B isoforms B''- ...PP2A subunit B isoform PR72/PR130 / PP2A subunit B isoform R3 isoform / PP2A subunit B isoforms B''-PR72/PR130 / PP2A subunit B isoforms B72/B130 / Serine/threonine-protein phosphatase 2A 72/130 kDa regulatory subunit B


Mass: 33963.355 Da / Num. of mol.: 2 / Fragment: PR72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R3A, PPP2R3 / Plasmid: Pet 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06190
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50:50 (0.1 M NaH2PO4/0.1 M K2HPO4, 0.1 M MES, 2 M NaCl) 8 mg/ml protein , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2006
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 20230 / Num. obs: 20230 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.076 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.609

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
CNSrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→34.926 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1036 5.12 %Random
Rwork0.2069 ---
obs0.2095 20215 99.65 %-
all-20215 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 4 0 4444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114579
X-RAY DIFFRACTIONf_angle_d0.896221
X-RAY DIFFRACTIONf_dihedral_angle_d13.5671674
X-RAY DIFFRACTIONf_chiral_restr0.059656
X-RAY DIFFRACTIONf_plane_restr0.003796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.05280.3211520.26042695X-RAY DIFFRACTION98
3.0528-3.24390.28461400.23552715X-RAY DIFFRACTION100
3.2439-3.49420.25591440.20652752X-RAY DIFFRACTION100
3.4942-3.84540.23681500.19452715X-RAY DIFFRACTION100
3.8454-4.4010.24611430.18842759X-RAY DIFFRACTION100
4.401-5.54120.25751480.20492759X-RAY DIFFRACTION100
5.5412-34.9290.25691590.20992784X-RAY DIFFRACTION100
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)
10.28690.14450.09080.1999-0.12490.1615-0.081-0.06650.01-0.1740.0652-0.14030.3486-0.13850.00080.32160.0341-0.03770.31230.00950.23356.1846-13.259738.1146
20.0481-0.0721-0.05340.3085-0.16540.4067-0.10610.22380.0478-0.36780.1952-0.1190.057-0.4170.06640.3131-0.0796-0.01770.2351-0.01630.19736.61840.573720.7641
30.06210.0096-0.04130.14210.12910.19180.2114-0.03510.2077-0.38830.2158-0.1855-0.28310.0230.60170.2785-0.36360.32480.03630.00820.824518.579713.240219.6405
40.18380.09960.28130.1127-0.02480.76940.1054-0.4828-0.0424-0.02310.2437-0.83050.27610.54620.24830.27360.0183-0.02720.5772-0.21160.601830.3782-8.629155.2113
50.01720.0237-0.0050.1042-0.05820.01510.0120.0048-0.296-0.08990.1274-0.594-0.2030.5906-0.00180.3565-0.11760.07040.6277-0.19030.491122.99018.728566.0097
60.0818-0.07390.0470.0703-0.0370.0330.22480.0938-0.0086-0.2260.0140.1068-0.59780.05730.00950.689-0.0320.07330.4704-0.13080.44037.398516.699760.9359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 172 through 289 )
2X-RAY DIFFRACTION2chain 'A' and (resid 290 through 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 443 )
4X-RAY DIFFRACTION4chain 'B' and (resid 172 through 289 )
5X-RAY DIFFRACTION5chain 'B' and (resid 290 through 372 )
6X-RAY DIFFRACTION6chain 'B' and (resid 373 through 443 )

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