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- PDB-2o8a: rat PP1cgamma complexed with mouse inhibitor-2 -

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Basic information

Entry
Database: PDB / ID: 2o8a
Titlerat PP1cgamma complexed with mouse inhibitor-2
Components
  • Protein phosphatase inhibitor 2
  • Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
KeywordsHYDROLASE/inhibitor / protein phosphatase / inhibitor-2 / HYDROLASE-inhibitor COMPLEX
Function / homology
Function and homology information


Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / RAF activation / Separation of Sister Chromatids / PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / RAF activation / Separation of Sister Chromatids / PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / protein phosphatase inhibitor activity / microtubule organizing center / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / molecular function inhibitor activity / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / phosphatase activity / cleavage furrow / blastocyst development / regulation of signal transduction / positive regulation of glial cell proliferation / protein dephosphorylation / circadian regulation of gene expression / neuron differentiation / regulation of circadian rhythm / kinetochore / presynapse / midbody / growth cone / postsynapse / spermatogenesis / protein phosphatase binding / mitochondrial outer membrane / dendritic spine / chromosome, telomeric region / nuclear speck / cell cycle / protein domain specific binding / cell division / glutamatergic synapse / protein-containing complex binding / nucleolus / protein kinase binding / protein-containing complex / mitochondrion / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1050 / Protein phosphatase inhibitor 2 (IPP-2) / Protein phosphatase inhibitor 2 (IPP-2) / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1050 / Protein phosphatase inhibitor 2 (IPP-2) / Protein phosphatase inhibitor 2 (IPP-2) / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Protein phosphatase inhibitor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsHurley, T.D.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis for regulation of protein phosphatase 1 by inhibitor-2.
Authors: Hurley, T.D. / Yang, J. / Zhang, L. / Goodwin, K.D. / Zou, Q. / Cortese, M. / Dunker, A.K. / Depaoli-Roach, A.A.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
I: Protein phosphatase inhibitor 2
B: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
J: Protein phosphatase inhibitor 2


Theoretical massNumber of molelcules
Total (without water)122,0244
Polymers122,0244
Non-polymers00
Water1,802100
1
A: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
I: Protein phosphatase inhibitor 2


Theoretical massNumber of molelcules
Total (without water)61,0122
Polymers61,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-14 kcal/mol
Surface area16170 Å2
MethodPISA, PQS
2
B: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
J: Protein phosphatase inhibitor 2


Theoretical massNumber of molelcules
Total (without water)61,0122
Polymers61,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-14 kcal/mol
Surface area16110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.462, 103.807, 151.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B
12I J

NCS domain segments:

Dom-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 2

Component-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA6 - 30012 - 306
21GLUGLUBC6 - 30012 - 306
12ASPASPIB12 - 16812 - 168
22ASPASPJD12 - 16812 - 168

NCS ensembles :
IDDetails
1A B
2I J

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Components

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


Mass: 37859.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1cc / Plasmid: pTACTAC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P63088, protein-serine/threonine phosphatase
#2: Protein Protein phosphatase inhibitor 2 / IPP-2


Mass: 23152.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp1r2 / Plasmid: pACYC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9DCL8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-HCL, 300 mM Sodium Acetate, 12% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→43 Å / Num. all: 46465 / Num. obs: 44514 / % possible obs: 95.8 % / Observed criterion σ(I): 0.2 / Redundancy: 5.3 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.077 / Net I/σ(I): 12.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3942 / Χ2: 1.175 / % possible all: 86

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PP1c gamma (human)

Resolution: 2.61→41.7 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.307 / SU ML: 0.177 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2248 5.1 %RANDOM
Rwork0.216 ---
all0.218 46465 --
obs0.218 44466 95.39 %-
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: 47.047 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--2.5 Å20 Å2
3----2.07 Å2
Refine analyze
FreeObs
Luzzati sigma a0.255 Å0.324 Å
Refinement stepCycle: LAST / Resolution: 2.61→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5742 0 0 100 5842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215858
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9697877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675699
X-RAY DIFFRACTIONr_chiral_restr0.0850.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024418
X-RAY DIFFRACTIONr_nbd_refined0.1960.22431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.29
X-RAY DIFFRACTIONr_mcbond_it0.5631.53509
X-RAY DIFFRACTIONr_mcangle_it1.16125636
X-RAY DIFFRACTIONr_scbond_it1.732349
X-RAY DIFFRACTIONr_scangle_it2.9534.52241
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1182TIGHT POSITIONAL0.030.05
1A1200MEDIUM POSITIONAL0.240.5
1A1182TIGHT THERMAL0.080.5
1A1200MEDIUM THERMAL0.52
2B232TIGHT POSITIONAL0.030.05
2B255MEDIUM POSITIONAL0.510.5
2B232TIGHT THERMAL0.050.5
2B255MEDIUM THERMAL0.312
LS refinement shellResolution: 2.61→2.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 151 -
Rwork0.294 2594 -
obs-2745 86 %

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