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- PDB-2y09: The cyanobacterial PP2C-like phosphatase tPphA requires three met... -

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Basic information

Entry
Database: PDB / ID: 2y09
TitleThe cyanobacterial PP2C-like phosphatase tPphA requires three metals in the catalytic center for efficient catalysis
ComponentsPROTEIN SERIN-THREONIN PHOSPHATASE
KeywordsHYDROLASE / PP2C FAMILY PHOSPHATASE
Function / homology
Function and homology information


protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / metal ion binding
Similarity search - Function
Protein phosphatase 2C / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 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-serine/threonine phosphatase
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchlicker, C. / Jiyong, S. / Forchhammer, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: A Third Metal is Required for Catalytic Activity of the Signal-Transducing Protein Phosphatase M Tppha.
Authors: Su, J. / Schlicker, C. / Forchhammer, K.
History
DepositionDec 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: PROTEIN SERIN-THREONIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8225
Polymers26,6931
Non-polymers1294
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.714, 151.678, 82.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2094-

HOH

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Components

#1: Protein PROTEIN SERIN-THREONIN PHOSPHATASE


Mass: 26692.965 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DGS1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 119 TO ALA

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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: 3 Å3/Da / Density % sol: 59.54 % / Description: NONE
Crystal growDetails: 30% PEG3350 0.2M CACL2 0.1M TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→36.33 Å / Num. obs: 27138 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 1 % / Biso Wilson estimate: 17.06 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.2
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.67 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J82

2j82


Resolution: 1.7→36.33 Å / SU ML: 0.17 / σ(F): 0.1 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1318 5 %
Rwork0.1923 --
obs0.1936 26135 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.638 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.3274 Å20 Å20 Å2
2--1.4321 Å20 Å2
3----3.7595 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 4 112 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071819
X-RAY DIFFRACTIONf_angle_d1.1272469
X-RAY DIFFRACTIONf_dihedral_angle_d13.782646
X-RAY DIFFRACTIONf_chiral_restr0.088285
X-RAY DIFFRACTIONf_plane_restr0.004327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76810.25771340.23572388X-RAY DIFFRACTION84
1.7681-1.84850.29311520.20652576X-RAY DIFFRACTION91
1.8485-1.9460.21691470.19432692X-RAY DIFFRACTION94
1.946-2.06790.18471480.17642742X-RAY DIFFRACTION97
2.0679-2.22750.21431350.17692809X-RAY DIFFRACTION98
2.2275-2.45170.19951460.18582842X-RAY DIFFRACTION99
2.4517-2.80630.20291650.19362845X-RAY DIFFRACTION99
2.8063-3.53520.22891420.1912935X-RAY DIFFRACTION100
3.5352-36.33870.21681490.19022988X-RAY DIFFRACTION98

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