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- PDB-2iq1: Crystal structure of human PPM1K -

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Basic information

Entry
Database: PDB / ID: 2iq1
TitleCrystal structure of human PPM1K
ComponentsProtein phosphatase 2C kappa, PPM1K
KeywordsHYDROLASE / protein phosphatase 2C kappa / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


[3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / [3-methyl-2-oxobutanoate dehydrogenase (lipoamide)]-phosphatase activity / regulation of intracellular signal transduction / H139Hfs13* PPM1K causes a mild variant of MSUD / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / regulation of mitochondrial membrane permeability involved in apoptotic process / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / manganese ion binding ...[3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / [3-methyl-2-oxobutanoate dehydrogenase (lipoamide)]-phosphatase activity / regulation of intracellular signal transduction / H139Hfs13* PPM1K causes a mild variant of MSUD / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / regulation of mitochondrial membrane permeability involved in apoptotic process / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / 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
Protein phosphatase Mn(2+)-dependent 1K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsBonanno, J.B. / Freeman, J. / Russell, M. / Bain, K.T. / Adams, J. / Pelletier, L. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2007
Title: Structural genomics of protein phosphatases
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 2C kappa, PPM1K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2242
Polymers30,1991
Non-polymers241
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.442, 69.406, 77.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein phosphatase 2C kappa, PPM1K / PP2C-like protein / Hypothetical protein DKFZp761G058


Mass: 30199.197 Da / Num. of mol.: 1 / Fragment: Residues 89-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp761G058 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8N3J5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8
Details: 100mM Hepes pH 8, 18% PEG 10K, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2006
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.25→51.674 Å / Num. all: 15773 / Num. obs: 15758 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 8 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.5 / Num. measured all: 17878 / Num. unique all: 2247 / Rsym value: 0.848 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHELXphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.821 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.237 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 785 5 %RANDOM
Rwork0.181 ---
obs0.184 15717 99.99 %-
all-15718 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.645 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2---0.02 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 1 126 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222025
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9532745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46224.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62115350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2071511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021524
X-RAY DIFFRACTIONr_nbd_refined0.2010.2903
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21380
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2147
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.29
X-RAY DIFFRACTIONr_mcbond_it1.0121.51313
X-RAY DIFFRACTIONr_mcangle_it1.70722063
X-RAY DIFFRACTIONr_scbond_it2.8223774
X-RAY DIFFRACTIONr_scangle_it4.5584.5679
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 53 -
Rwork0.211 1082 -
obs-1135 99.91 %

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