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- PDB-3fxk: Crystal Structure of Human Protein phosphatase 1A (PPM1A) Bound w... -

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Basic information

Entry
Database: PDB / ID: 3fxk
TitleCrystal Structure of Human Protein phosphatase 1A (PPM1A) Bound with Phosphate at 10 mM of Mn2+
ComponentsProtein phosphatase 1A
KeywordsHYDROLASE / phosphatase / Alternative splicing / Magnesium / Manganese / Metal-binding / Phosphoprotein / Protein phosphatase
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 / dephosphorylation / negative regulation of canonical NF-kappaB signal transduction / 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 / magnesium ion binding / negative regulation of transcription by RNA polymerase II / 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
: / PHOSPHATE ION / Protein phosphatase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsHu, T. / Wang, L. / Wang, K. / Jiang, H. / Shen, X.
CitationJournal: To be published
Title: Structural basis for the Mn2+-dependent activation of human PPM1A
Authors: Hu, T. / Wang, L. / Wang, K. / Chen, J. / Jiang, H. / Shen, X.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Protein phosphatase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8745
Polymers43,5741
Non-polymers3004
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.760, 90.760, 105.711
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein phosphatase 1A / PPM1A / Protein phosphatase 2C isoform alpha / PP2C-alpha / IA


Mass: 43573.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 50mM potassium phosphate, 12%(w/v) PEG8000, 15%(v/v) glycerol, 2mM DTT, 10mM MnCl2, pH 5.2, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→27.832 Å / Num. obs: 29451 / % possible obs: 98.8 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 10.18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.219.70.3532.24112242400.35398.3
2.21-2.359.70.272.63838539610.2798.2
2.35-2.519.70.1824.23658237790.18298.6
2.51-2.719.70.135.93406935270.1398.7
2.71-2.979.60.0868.83155132710.08699.1
2.97-3.329.60.05612.92858729790.05699.1
3.32-3.839.50.03817.82505226240.03899.4
3.83-4.79.40.03119.72141322700.03199.6
4.7-6.649.30.0318.81656217820.0399.7
6.64-27.838.70.02918.6888910180.02998.3

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 4.109 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1486 5.1 %RANDOM
Rwork0.196 ---
obs0.198 29362 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.79 Å2 / Biso mean: 27.384 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 12 313 3153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212893
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9593909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58824.61141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92715502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9881519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022217
X-RAY DIFFRACTIONr_nbd_refined0.2060.21410
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.211
X-RAY DIFFRACTIONr_mcbond_it0.6831.51852
X-RAY DIFFRACTIONr_mcangle_it1.17122900
X-RAY DIFFRACTIONr_scbond_it1.92331152
X-RAY DIFFRACTIONr_scangle_it3.1694.51008
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 86 -
Rwork0.217 2015 -
all-2101 -
obs--97.77 %

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