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- PDB-6ak7: Crystal structure of PPM1K-N94K -

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Basic information

Entry
Database: PDB / ID: 6ak7
TitleCrystal structure of PPM1K-N94K
ComponentsProtein phosphatase 1K, mitochondrial
KeywordsHYDROLASE / phosphatase / BDP / ppm
Function / homology
Function and homology information


[3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / [3-methyl-2-oxobutanoate dehydrogenase (lipoamide)]-phosphatase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / regulation of mitochondrial membrane permeability involved in apoptotic process / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / manganese ion binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Sigma factor PP2C-like phosphatases / 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 ...Sigma factor PP2C-like phosphatases / 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 / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Protein phosphatase Mn(2+)-dependent 1K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å
AuthorsMeisam, R.D. / Guo, L.L. / Xiao, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470789 China
National Natural Science Foundation of China31611540337 China
National Natural Science Foundation of China81773704 China
CitationJournal: To Be Published
Title: Structure of PPM1K-N94K mutant at 2.61 Angstroms resolution
Authors: Meisam, R.D. / Guo, L.L. / Xiao, P.
History
DepositionAug 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 1K, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4528
Polymers28,1211
Non-polymers3327
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-35 kcal/mol
Surface area11580 Å2
Unit cell
Length a, b, c (Å)122.784, 122.784, 61.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

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Components

#1: Protein Protein phosphatase 1K, mitochondrial / PP2C domain-containing protein phosphatase 1K / PP2C-like mitochondrial protein / PP2C-type ...PP2C domain-containing protein phosphatase 1K / PP2C-like mitochondrial protein / PP2C-type mitochondrial phosphoprotein phosphatase / PTMP / Protein phosphatase 2C isoform kappa / PP2C-kappa


Mass: 28120.877 Da / Num. of mol.: 1 / Mutation: N94K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1K, PP2CM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8N3J5, protein-serine/threonine phosphatase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 4.77 Å3/Da / Density % sol: 74.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 12% PEG 3350, 0.2 M MgCl2, 10 mM Mercaptoethanol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→35.5 Å / Num. obs: 16613 / % possible obs: 99.6 % / Redundancy: 9.4 % / Net I/σ(I): 0.3
Reflection shellResolution: 2.6→2.69 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DA1

4da1


Resolution: 2.605→35.445 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.15
RfactorNum. reflection% reflection
Rfree0.2243 810 4.89 %
Rwork0.1924 --
obs0.1939 16569 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.8 Å2 / Biso mean: 47.1155 Å2 / Biso min: 27.73 Å2
Refinement stepCycle: final / Resolution: 2.605→35.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 16 104 2089
Biso mean--64.39 48.78 -
Num. residues----257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.605-2.76820.29531460.27242561270799
2.7682-2.98180.32721240.246126082732100
2.9818-3.28170.24231340.21542595272999
3.2817-3.75610.22991160.185826282744100
3.7561-4.73060.17941490.15526532802100
4.7306-35.4480.21281410.18427142855100

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