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- PDB-1jk7: CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PRO... -

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Basic information

Entry
Database: PDB / ID: 1jk7
TitleCRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1
ComponentsSERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
KeywordsHYDROLASE/TOXIN / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE-TOXIN 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 / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod ...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 / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / phosphatase activity / cleavage furrow / microtubule organizing center / phosphoprotein phosphatase activity / mitotic sister chromatid segregation / blastocyst development / positive regulation of glial cell proliferation / protein dephosphorylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / circadian regulation of gene expression / RHO GTPases Activate Formins / RAF activation / regulation of circadian rhythm / kinetochore / neuron differentiation / Separation of Sister Chromatids / : / presynapse / MAPK cascade / midbody / spermatogenesis / dendritic spine / mitochondrial outer membrane / nuclear speck / protein domain specific binding / cell division / focal adhesion / protein kinase binding / protein-containing complex binding / nucleolus / glutamatergic synapse / protein-containing complex / mitochondrion / RNA binding / metal ion binding / nucleus / cytoplasm / cytosol
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
BETA-MERCAPTOETHANOL / : / OKADAIC ACID / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaynes, J.T. / Bateman, K.S. / Cherney, M.M. / Das, A.K. / James, M.N.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of the tumor-promoter okadaic acid bound to protein phosphatase-1.
Authors: Maynes, J.T. / Bateman, K.S. / Cherney, M.M. / Das, A.K. / Luu, H.A. / Holmes, C.F. / James, M.N.
History
DepositionJul 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 16, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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.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_conn.ptnr2_label_seq_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 PP1-GAMMA CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2768
Polymers37,0311
Non-polymers1,2457
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.180, 99.180, 62.170
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-2058-

HOH

21A-2189-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G


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

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Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OKA / OKADAIC ACID / 9,10-DEEPITHIO-9,10-DIDEHYDROACANTHIFOLICIN


Mass: 805.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H68O13
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsThe Okadaic Acid was obtained from DINOFLAGELLATE, PROROCENTRUM LIMA.

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: LITHIUM SULPHATE, PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.4 mMprotein1drop
22 Mlithium sulfate1reservoir
3100 mMTris1reservoirpH8.0
42 %PEG4001reservoir
510 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2000 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 24439 / Num. obs: 24439 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.46 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 30
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.33 % / Rmerge(I) obs: 0.358 / % possible all: 95.4
Reflection
*PLUS
Num. measured all: 434544
Reflection shell
*PLUS
% possible obs: 95.4 % / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJM

1fjm


Resolution: 1.9→29.66 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2611346.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1417 5.8 %RANDOM
Rwork0.199 ---
all0.199 24439 --
obs0.199 24439 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.6197 Å2 / ksol: 0.384153 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 69 172 2614
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.243 122 5.2 %
Rwork0.218 2216 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DAM.PARAMDAM.TOP
X-RAY DIFFRACTION2BME.PARAMBME.TOP
X-RAY DIFFRACTION3ION.PARAMPROTEIN.TOP
X-RAY DIFFRACTION4PROTEIN_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.243 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.218

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