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- PDB-1a6q: CRYSTAL STRUCTURE OF THE PROTEIN SERINE/THREONINE PHOSPHATASE 2C ... -

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Basic information

Entry
Database: PDB / ID: 1a6q
TitleCRYSTAL STRUCTURE OF THE PROTEIN SERINE/THREONINE PHOSPHATASE 2C AT 2 A RESOLUTION
ComponentsPHOSPHATASE 2C
KeywordsHYDROLASE / CATALYTIC MECHANISM / METALLOENZYME / PROTEIN PHOSPHATASE 2C / SIGNAL TRANSDUCTUIN
Function / homology
Function and homology information


N-terminal protein myristoylation / calmodulin-dependent protein phosphatase activity / Energy dependent regulation of mTOR by LKB1-AMPK / dephosphorylation / regulation of canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / R-SMAD binding / negative regulation of BMP signaling pathway ...N-terminal protein myristoylation / calmodulin-dependent protein phosphatase activity / Energy dependent regulation of mTOR by LKB1-AMPK / dephosphorylation / regulation of canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / R-SMAD binding / negative regulation of BMP signaling pathway / cellular response to transforming growth factor beta stimulus / protein dephosphorylation / negative regulation of canonical NF-kappaB signal transduction / protein export from nucleus / positive regulation of protein export from nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of canonical Wnt signaling pathway / manganese ion binding / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Phosphatase 2C, C-terminal domain suprefamily / Protein serine/threonine phosphatase 2C, C-terminal / Phosphatase 2C, C-terminal domain superfamily / Protein serine/threonine phosphatase 2C, C-terminal domain / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family ...Phosphatase 2C, C-terminal domain suprefamily / Protein serine/threonine phosphatase 2C, C-terminal / Phosphatase 2C, C-terminal domain superfamily / Protein serine/threonine phosphatase 2C, C-terminal domain / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Protein phosphatase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsDas, A.K. / Helps, N.R. / Cohen, P.T.W. / Barford, D.
CitationJournal: EMBO J. / Year: 1996
Title: Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution.
Authors: Das, A.K. / Helps, N.R. / Cohen, P.T. / Barford, D.
History
DepositionFeb 27, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Advisory / Derived calculations
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _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 / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATASE 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7084
Polymers42,5031
Non-polymers2053
Water3,657203
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.020, 91.020, 105.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHOSPHATASE 2C


Mass: 42502.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P35813, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 277 K / pH: 5
Details: 8-12% PEG8K,15% GLYCEROL, 50MM K-PO4, PH=5.0, 2 MM DTT AT 4 DEGREES C, temperature 277K
Crystal grow
*PLUS
Temperature: 100 K / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMpotassium phosphate1reservoir
28-12 %PEG80001reservoir
315 %(v/v)glycerol1reservoir
42 mMdithiothreitol1reservoir
510 mMTris-HCl1drop
650 mM1dropNaCl
71 mM1dropMn2+
82 mMdithiothreitol1drop
915 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BL19 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 9, 1996 / Details: MIRRORS
RadiationMonochromator: DARESBURY / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 33176 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 12.6
Reflection
*PLUS
Num. measured all: 215022

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.82refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rwork0.214 --
obs0.214 21806 -
Rfree--RANDOM
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 7 203 3031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.643
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.984
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH.WATER
X-RAY DIFFRACTION3PARAM.PHOSPHATETOP.PHOSPHATE
Software
*PLUS
Name: X-PLOR / Version: 3.82 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.37
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.984

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