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- PDB-4rag: CRYSTAL STRUCTURE of PPC2A-D38K -

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Basic information

Entry
Database: PDB / ID: 4rag
TitleCRYSTAL STRUCTURE of PPC2A-D38K
ComponentsProtein phosphatase 1A
KeywordsMETAL BINDING PROTEIN / serine/threonine phosphatase / PP2C family / phosphatation
Function / homology
Function and homology information


N-terminal protein myristoylation / calmodulin-dependent protein phosphatase activity / peptidyl-threonine dephosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of non-canonical NF-kappaB signal transduction / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / R-SMAD binding / negative regulation of BMP signaling pathway ...N-terminal protein myristoylation / calmodulin-dependent protein phosphatase activity / peptidyl-threonine dephosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of non-canonical NF-kappaB signal transduction / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / R-SMAD binding / negative regulation of BMP signaling pathway / negative regulation of canonical NF-kappaB signal transduction / dephosphorylation / cellular response to transforming growth factor beta stimulus / protein export from nucleus / protein dephosphorylation / 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 / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / membrane / nucleus / 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
: / Protein phosphatase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPan, C. / Tang, J.Y. / Xu, Y.F. / Xiao, P. / Liu, H.D. / Wang, H.A. / Wang, W.B. / Meng, F.G. / Yu, X. / Sun, J.P.
CitationJournal: Sci Rep / Year: 2015
Title: The catalytic role of the M2 metal ion in PP2C alpha
Authors: Pan, C. / Tang, J.Y. / Xu, Y.F. / Xiao, P. / Liu, H.D. / Wang, H.A. / Wang, W.B. / Meng, F.G. / Yu, X. / Sun, J.P.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Protein phosphatase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8272
Polymers40,7721
Non-polymers551
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.817, 90.817, 105.408
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

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Components

#1: Protein Protein phosphatase 1A / Protein phosphatase 2C isoform alpha / PP2C-alpha / Protein phosphatase IA


Mass: 40772.016 Da / Num. of mol.: 1 / Fragment: PP2Ca, UNP residues 2-368 / Mutation: D38K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1A, PPPM1A / Production host: Escherichia coli (E. coli) / Strain (production host): bl21
References: UniProt: P35813, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15%(v/v) PEG8000, pH 5.5, 50mM K2HPO4, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: SYNTEX / Detector: DIFFRACTOMETER / Date: Mar 30, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 43274 / Num. obs: 43274 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.85-1.88199.9
1.88-1.921100
1.92-1.951100
1.95-1.99199.9
1.99-2.04199.9
2.04-2.081100
2.08-2.141100
2.14-2.191100
2.19-2.261100
2.26-2.33199.9
2.33-2.411100
2.41-2.51199.9
2.51-2.631100
2.63-2.761100
2.76-2.94199.8
2.94-3.161100
3.16-3.481100
3.48-3.991100
3.99-5.02199.7
5.02-50199.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A6Q
Resolution: 1.85→36.844 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 2175 5.04 %RANDOM
Rwork0.1991 ---
all0.2006 45338 --
obs0.2006 43163 99.55 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.141 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4984 Å20 Å20 Å2
2--0.4984 Å2-0 Å2
3----0.9968 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 1 219 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062873
X-RAY DIFFRACTIONf_angle_d1.1033878
X-RAY DIFFRACTIONf_dihedral_angle_d13.9211082
X-RAY DIFFRACTIONf_chiral_restr0.08419
X-RAY DIFFRACTIONf_plane_restr0.004516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8502-1.91630.26812290.2512399099
1.9163-1.99310.22872270.2277402799
1.9931-2.08380.23132120.20484076100
2.0838-2.19360.21542230.20354045100
2.1936-2.3310.23691830.2064120100
2.331-2.5110.23452160.2054088100
2.511-2.76360.28852110.21314136100
2.7636-3.16330.22342130.20634129100
3.1633-3.98470.22822500.18424128100
3.9847-36.85160.21342110.191424998

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