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- PDB-4mew: Structure of the core fragment of human PR70 -

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Basic information

Entry
Database: PDB / ID: 4mew
TitleStructure of the core fragment of human PR70
ComponentsSerine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta
Keywordshydrolase / cell cycle / EF-hands / Protein Phosphatase / Calcium Binding / METAL BINDING PROTEIN
Function / homology
Function and homology information


protein phosphatase type 2A complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / protein phosphatase regulator activity / Cyclin A/B1/B2 associated events during G2/M transition / protein dephosphorylation / Cyclin D associated events in G1 / regulation of cell cycle / calcium ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Recoverin; domain 1 - #230 / 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 ...Recoverin; domain 1 - #230 / 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 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.993 Å
AuthorsDovega, R.B. / Quistgaard, E.M. / Tsutakawa, S. / Anandapadamanaban, M. / Low, C. / Nordlund, P.
CitationJournal: Plos One / Year: 2014
Title: Structural and Biochemical Characterization of Human PR70 in Isolation and in Complex with the Scaffolding Subunit of Protein Phosphatase 2A.
Authors: Dovega, R. / Tsutakawa, S. / Quistgaard, E.M. / Anandapadamanaban, M. / Low, C. / Nordlund, P.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1305
Polymers41,8661
Non-polymers2644
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.11, 74.46, 62.33
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta / PP2A subunit B isoform PR48 / Protein phosphatase 2A 48 kDa regulatory subunit


Mass: 41866.066 Da / Num. of mol.: 1 / Fragment: Residues 130-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R3B, PPP2R3L / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9Y5P8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Tris-HCl, 16% PEG 2000 monomethyl ether, 0.15 M trimethylamine N-oxide, pH 7.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.99→37.23 Å / Num. all: 45116 / Num. obs: 45116 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.097 / Net I/σ(I): 13.8
Reflection shellResolution: 1.99→2.04 Å / Mean I/σ(I) obs: 2.42 / Num. unique all: 3010 / Rsym value: 0.601 / % possible all: 89

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(autosol)model building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(autosol)phasing
RefinementMethod to determine structure: SAD / Resolution: 1.993→37.23 Å / SU ML: 0.2 / σ(F): 1.51 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 958 4.13 %Random
Rwork0.1621 ---
obs0.1635 45105 99.07 %-
all-45105 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.993→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 14 347 3205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042925
X-RAY DIFFRACTIONf_angle_d0.8033949
X-RAY DIFFRACTIONf_dihedral_angle_d13.4171071
X-RAY DIFFRACTIONf_chiral_restr0.064420
X-RAY DIFFRACTIONf_plane_restr0.003508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9931-2.0470.3051050.2363040X-RAY DIFFRACTION89
2.047-2.10720.24091480.20513341X-RAY DIFFRACTION100
2.1072-2.17530.20771330.1873389X-RAY DIFFRACTION100
2.1753-2.2530.26831120.1853364X-RAY DIFFRACTION100
2.253-2.34320.21781440.17853356X-RAY DIFFRACTION100
2.3432-2.44980.24131480.17163367X-RAY DIFFRACTION100
2.4498-2.57890.24491450.17073314X-RAY DIFFRACTION100
2.5789-2.74050.21521470.16313367X-RAY DIFFRACTION100
2.7405-2.9520.18631420.16963371X-RAY DIFFRACTION100
2.952-3.24890.18871520.15983318X-RAY DIFFRACTION100
3.2489-3.71860.18091310.13623414X-RAY DIFFRACTION100
3.7186-4.68360.13541790.12713300X-RAY DIFFRACTION100
4.6836-37.23650.16911770.15773301X-RAY DIFFRACTION99
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)
11.2688-0.3349-1.11840.75990.89122.1704-0.05060.0062-0.0516-0.0164-0.01660.02240.120.08590.02970.088-0.0113-0.02950.1070.00270.101245.028431.55267.2065
21.22010.2335-1.03940.5763-0.67442.18960.0665-0.04250.12390.0152-0.00620.0847-0.1189-0.1166-0.03080.11530.01520.00170.1081-0.01820.126425.247442.53634.4843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resseq 134:309)
2X-RAY DIFFRACTION2(chain 'A' and resseq 310:481)

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