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- PDB-2bcd: X-ray crystal structure of Protein Phosphatase-1 with the marine ... -

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Basic information

Entry
Database: PDB / ID: 2bcd
TitleX-ray crystal structure of Protein Phosphatase-1 with the marine toxin motuporin bound
Components
  • MOTUPORIN
  • Serine/threonine protein phosphatase PP1-gamma catalytic subunit
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein phosphtase / natural product inhibitors / motuporin / nodularin / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / microtubule organizing center / protein serine/threonine phosphatase activity / glycogen metabolic process / myosin phosphatase activity ...PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / microtubule organizing center / protein serine/threonine phosphatase activity / glycogen metabolic process / myosin phosphatase activity / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / Maturation of hRSV A proteins / phosphatase activity / mitotic sister chromatid segregation / cleavage furrow / phosphoprotein phosphatase activity / blastocyst development / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of glial cell proliferation / Resolution of Sister Chromatid Cohesion / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / RHO GTPases Activate Formins / RAF activation / circadian regulation of gene expression / regulation of circadian rhythm / neuron differentiation / kinetochore / Separation of Sister Chromatids / MAPK cascade / Circadian Clock / presynapse / midbody / spermatogenesis / mitochondrial outer membrane / dendritic spine / nuclear speck / protein domain specific binding / cell division / focal adhesion / glutamatergic synapse / protein-containing complex binding / nucleolus / protein kinase binding / protein-containing complex / mitochondrion / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...: / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
motuporin / BETA-MERCAPTOETHANOL / : / : / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
marine sponge Thenonella swinhoie grey (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaynes, J.T. / Luu, H.A. / Cherney, M.M. / Andersen, R.J. / Williams, D. / Holmes, C.F. / James, M.N.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Protein Phosphatase-1 Bound to Motuporin and Dihydromicrocystin-LA: Elucidation of the Mechanism of Enzyme Inhibition by Cyanobacterial Toxins.
Authors: Maynes, J.T. / Luu, H.A. / Cherney, M.M. / Andersen, R.J. / Williams, D. / Holmes, C.F. / James, M.N.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jul 27, 2011Group: Database references
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_validate_polymer_linkage / struct_conn
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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine protein phosphatase PP1-gamma catalytic subunit
B: MOTUPORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,41212
Polymers37,8172
Non-polymers59610
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.955, 100.955, 63.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-403-

MN

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Components

#1: Protein Serine/threonine protein phosphatase PP1-gamma catalytic subunit / PP-1G / Protein phosphatase 1C catalytic subunit


Mass: 37030.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CC / Production host: Escherichia coli (E. coli)
References: UniProt: P36873, protein-serine/threonine phosphatase
#2: Protein/peptide MOTUPORIN


Type: Cyclic peptide / Class: Toxin / Mass: 785.922 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) marine sponge Thenonella swinhoie grey (invertebrata)
References: NOR: NOR00825, motuporin
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%), beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.13 Å / Num. obs: 19722 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.21 Å / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 2821 / Rsym value: 0.293 / % possible all: 100

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Phasing

Phasing MRRfactor: 37.1 / Cor.coef. Fo:Fc: 69.6 / Cor.coef. Io to Ic: 62.1
Highest resolutionLowest resolution
Rotation3 Å100 Å
Translation3 Å20 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1JK7

1jk7


Resolution: 2.1→31.75 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.421 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.253 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1008 5.1 %RANDOM
Rwork0.221 ---
all0.223 ---
obs0.223 19682 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.439 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 16 73 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222477
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9923331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60924.034119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03415416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6971516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021892
X-RAY DIFFRACTIONr_nbd_refined0.1550.31002
X-RAY DIFFRACTIONr_nbtor_refined0.30.51631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.5188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.56
X-RAY DIFFRACTIONr_mcbond_it0.9261.51519
X-RAY DIFFRACTIONr_mcangle_it1.48622342
X-RAY DIFFRACTIONr_scbond_it2.11631110
X-RAY DIFFRACTIONr_scangle_it2.9434.5989
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 83 -
Rwork0.246 1331 -
all-1414 -
obs-2821 100 %

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