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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 / homologyPPM-type phosphatase domain / Protein serine/threonine phosphatase 2C, C-terminal domain / PPM-type phosphatase, divalent cation binding / Protein phosphatase 2C family / PPM-type phosphatase domain superfamily / Protein serine/threonine phosphatase 2C, C-terminal / Protein phosphatase 2C / Phosphatase 2C, C-terminal domain superfamily / PPM-type phosphatase domain signature. / Downregulation of SMAD2/3:SMAD4 transcriptional activity ...PPM-type phosphatase domain / Protein serine/threonine phosphatase 2C, C-terminal domain / PPM-type phosphatase, divalent cation binding / Protein phosphatase 2C family / PPM-type phosphatase domain superfamily / Protein serine/threonine phosphatase 2C, C-terminal / Protein phosphatase 2C / Phosphatase 2C, C-terminal domain superfamily / PPM-type phosphatase domain signature. / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Energy dependent regulation of mTOR by LKB1-AMPK / PPM-type phosphatase domain profile. / calmodulin-dependent protein phosphatase activity / N-terminal protein myristoylation / negative regulation of SMAD protein complex assembly / peptidyl-threonine dephosphorylation / negative regulation of NIK/NF-kappaB signaling / magnesium-dependent protein serine/threonine phosphatase activity / R-SMAD binding / negative regulation of BMP signaling pathway / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / dephosphorylation / cellular response to transforming growth factor beta stimulus / negative regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of protein export from nucleus / protein dephosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of canonical Wnt signaling pathway / cell cycle arrest / positive regulation of I-kappaB kinase/NF-kappaB signaling / manganese ion binding / positive regulation of transcription, DNA-templated / magnesium ion binding / negative regulation of transcription by RNA polymerase II / membrane / nucleoplasm / plasma membrane / nucleus / cytosol / Protein phosphatase 1A
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 2 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 27, 1998 / Release: May 27, 1998
RevisionDateData content typeGroupProviderType
1.0May 27, 1998Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jul 27, 2011Structure modelAdvisory / Derived calculations
Remark 285 THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE ... THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE CRYSTAL AU, APPLY THE FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. X0 1 0.500300 0.865850 0.001430 45.442970 X0 2 0.865850 -0.500300 0.000160 78.817080 X0 3 0.000850 0.001160 -1.000000 88.012550 CRYSTAL AU = (X0) * CHAINS A

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATASE 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7084
Polyers42,5031
Non-polymers2053
Water3,657203
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 31 2 1

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Components

#1: Protein/peptide PHOSPHATASE 2C


Mass: 42502.703 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Genus (production host): Escherichia / 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 / Formula: Mn / Manganese
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Formula: H2O / Water

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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 / Density percent sol: 59 %
Crystal growTemp: 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
Temp: 100 K / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE BL19 / Synchrotron site: ESRF / Beamline: BL19 / Wavelength: 0.87
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Feb 9, 1996
RadiationMonochromator: DARESBURY / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 15 Å / Number obs: 33176 / Observed criterion sigma I: 2 / Rmerge I obs: 0.089 / Rsym value: 0.089 / NetI over sigmaI: 12.6 / Redundancy: 6.5 % / Percent possible obs: 95.5
Reflection
*PLUS
Number measured all: 215022

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.82refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MIR / R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / Sigma F: 2
Least-squares processR factor R work: 0.214 / R factor obs: 0.214 / Highest resolution: 2 Å / Lowest resolution: 6 Å / Number reflection obs: 21806
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 2821 / Nucleic acid: 0 / Ligand: 7 / Solvent: 203 / Total: 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
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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