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- PDB-2p8e: Crystal structure of the serine/threonine phosphatase domain of h... -

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Basic information

Entry
Database: PDB / ID: 2p8e
TitleCrystal structure of the serine/threonine phosphatase domain of human PPM1B
ComponentsPPM1B beta isoform variant 6
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


N-terminal protein myristoylation / negative regulation of defense response to virus / peptidyl-threonine dephosphorylation / ALK mutants bind TKIs / negative regulation of interferon-beta production / regulation of canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / protein dephosphorylation ...N-terminal protein myristoylation / negative regulation of defense response to virus / peptidyl-threonine dephosphorylation / ALK mutants bind TKIs / negative regulation of interferon-beta production / regulation of canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / protein dephosphorylation / negative regulation of canonical NF-kappaB signal transduction / ISG15 antiviral mechanism / Signaling by ALK fusions and activated point mutants / positive regulation of canonical Wnt signaling pathway / manganese ion binding / nucleolus / magnesium ion binding / nucleus / membrane / cytosol
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
Protein phosphatase 1B / Protein phosphatase 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.816 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Lau, C. / Xu, W. / Smith, D. / 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
DepositionMar 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
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_conn_type / 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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 1.6Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT A MONOMER IS PROBABLY THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PPM1B beta isoform variant 6
B: PPM1B beta isoform variant 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6594
Polymers68,6112
Non-polymers492
Water7,764431
1
A: PPM1B beta isoform variant 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3302
Polymers34,3051
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PPM1B beta isoform variant 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3302
Polymers34,3051
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.399, 92.315, 118.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsprobable monomer

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Components

#1: Protein PPM1B beta isoform variant 6 / Protein phosphatase 2C isoform beta / PP2C-beta


Mass: 34305.309 Da / Num. of mol.: 2 / Fragment: serine/threonine phosphatase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1B / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4J6C0, UniProt: O75688*PLUS, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Hepes pH 7.5, 20% PEG 4000, 10% Isopropanol, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.816→72.932 Å / Num. all: 49509 / Num. obs: 49509 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.184 / Rsym value: 0.184 / Net I/σ(I): 8.3
Reflection shellResolution: 1.816→1.91 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6430 / Rsym value: 0.842 / % possible all: 84.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A6Q

1a6q


Resolution: 1.816→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.224 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2523 5.1 %RANDOM
Rwork0.186 ---
obs0.189 49432 93.8 %-
all-49432 --
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: 22.186 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.33 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.816→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 2 431 4871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214532
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9396138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08524.188234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5715770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1261534
X-RAY DIFFRACTIONr_chiral_restr0.1080.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023506
X-RAY DIFFRACTIONr_nbd_refined0.2090.22084
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2391
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.241
X-RAY DIFFRACTIONr_mcbond_it1.0391.52868
X-RAY DIFFRACTIONr_mcangle_it1.57824480
X-RAY DIFFRACTIONr_scbond_it2.68931899
X-RAY DIFFRACTIONr_scangle_it4.0394.51651
LS refinement shellResolution: 1.816→1.863 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 158 -
Rwork0.271 3038 -
obs-3196 83.53 %

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