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

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Basic information

Entry
Database: PDB / ID: 3fxm
TitleCrystal Structure of Human Protein phosphatase 1A (PPM1A) Bound with Citrate 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 / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / calmodulin-dependent protein phosphatase activity / dephosphorylation / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / R-SMAD binding / negative regulation of BMP signaling pathway ...N-terminal protein myristoylation / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / calmodulin-dependent protein phosphatase activity / dephosphorylation / 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 / negative regulation of transcription by RNA polymerase II / magnesium ion binding / 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
CITRATE ANION / : / PHOSPHATE ION / Protein phosphatase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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)43,9685
Polymers43,5741
Non-polymers3944
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.069, 91.069, 106.508
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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.93 Å3/Da / Density % sol: 57.96 % / Mosaicity: 0.64 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 50mM trisodium citrate, 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: 2.5→14.97 Å / Num. obs: 17595 / % possible obs: 97.5 % / Redundancy: 7.06 % / Rmerge(I) obs: 0.153 / Χ2: 1.3 / Scaling rejects: 6659
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.5-2.597.340.36521284617330.9197.9
2.59-2.697.30.3512.11290517520.9998.5
2.69-2.817.280.312.41298617591.0798.4
2.81-2.967.250.2692.71294117491.1698.5
2.96-3.147.180.2293.21306917651.3398.7
3.14-3.397.030.1784.11305817581.5198.4
3.39-3.726.910.1325.51311317431.6397.1
3.72-4.256.870.1056.81332217711.5697
4.25-5.316.810.0828.41320317721.4797
5.31-14.976.630.0789.11338517931.4394.2

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.5→14.97 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 8.368 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 895 5.1 %RANDOM
Rwork0.183 ---
obs0.186 17593 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.07 Å2 / Biso mean: 23.52 Å2 / Biso min: 2.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.16 Å20 Å2
2---0.31 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 20 273 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212901
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9613920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9735363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37124.61141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69115502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7571519
X-RAY DIFFRACTIONr_chiral_restr0.1010.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022229
X-RAY DIFFRACTIONr_nbd_refined0.220.21476
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.211
X-RAY DIFFRACTIONr_mcbond_it0.5411.51841
X-RAY DIFFRACTIONr_mcangle_it0.98222905
X-RAY DIFFRACTIONr_scbond_it1.51831160
X-RAY DIFFRACTIONr_scangle_it2.6174.51014
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 71 -
Rwork0.247 1182 -
all-1253 -
obs--98.27 %

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