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- PDB-1it6: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATA... -

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Basic information

Entry
Database: PDB / ID: 1it6
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATALYTIC SUBUNIT OF PROTEIN PHOSPHATASE 1
ComponentsSERINE/THREONINE PROTEIN PHOSPHATASE 1 GAMMA (PP1-GAMMA) CATALYTIC SUBUNIT
KeywordsHYDROLASE / 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 / 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 / microtubule organizing center / cleavage furrow / 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
CALYCULIN A / : / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKita, A. / Matsunaga, S. / Takai, A. / Kataiwa, H. / Wakimoto, T. / Fusetani, N. / Isobe, M. / Miki, K.
CitationJournal: Structure / Year: 2002
Title: Crystal structure of the complex between calyculin A and the catalytic subunit of protein phosphatase 1.
Authors: Kita, A. / Matsunaga, S. / Takai, A. / Kataiwa, H. / Wakimoto, T. / Fusetani, N. / Isobe, M. / Miki, K.
History
DepositionJan 9, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...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 / 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_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

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Assembly

Deposited unit
A: SERINE/THREONINE PROTEIN PHOSPHATASE 1 GAMMA (PP1-GAMMA) CATALYTIC SUBUNIT
B: SERINE/THREONINE PROTEIN PHOSPHATASE 1 GAMMA (PP1-GAMMA) CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3008
Polymers74,0622
Non-polymers2,2386
Water1,72996
1
A: SERINE/THREONINE PROTEIN PHOSPHATASE 1 GAMMA (PP1-GAMMA) CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1504
Polymers37,0311
Non-polymers1,1193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SERINE/THREONINE PROTEIN PHOSPHATASE 1 GAMMA (PP1-GAMMA) CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1504
Polymers37,0311
Non-polymers1,1193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.090, 136.360, 61.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SERINE/THREONINE PROTEIN PHOSPHATASE 1 GAMMA (PP1-GAMMA) CATALYTIC SUBUNIT


Mass: 37030.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P36873, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CYU / CALYCULIN A


Mass: 1009.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H81N4O15P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: PEG3350, POTASSIUM SULFATE, MANGANESE(II) CHLORIDE, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.4 mg/mlprotein1drop
210 mMTris-HCl1droppH7.8
30.3 M1dropNaCl
40.2 mM1dropMnCl2
53 mMdithiothreitol1drop
610 mMTris-HCl1reservoirpH7.8
720 %PEG33501reservoir
80.2 Mpotassium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 56617 / Num. obs: 56530 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 6.2 % / Num. measured all: 536140 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJM

1fjm


Resolution: 2→20 Å / Isotropic thermal model: ISOTROPIC / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.218 2510 RANDOM
Rwork0.182 --
all-56406 -
obs-49453 -
Displacement parametersBiso mean: 21.05 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 116 96 4936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.43
X-RAY DIFFRACTIONx_improper_angle_d1.098
Refinement
*PLUS
Rfactor obs: 0.182 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.43
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.098

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