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

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Basic information

Entry
Database: PDB / ID: 2xzv
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: 1.6 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.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.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
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.646, 151.436, 82.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 193 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 HEPES PH 7.4

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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: 1.6→36.26 Å / Num. obs: 30657 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 1 % / Biso Wilson estimate: 20.19 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.64
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 76.2

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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: 1.6→36.258 Å / SU ML: 0.21 / σ(F): 0.03 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1453 5 %
Rwork0.2098 --
obs0.2115 28942 88.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.46 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-8.0627 Å20 Å20 Å2
2---0.3672 Å20 Å2
3----7.6955 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 4 99 1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071810
X-RAY DIFFRACTIONf_angle_d1.0192456
X-RAY DIFFRACTIONf_dihedral_angle_d13.714637
X-RAY DIFFRACTIONf_chiral_restr0.077279
X-RAY DIFFRACTIONf_plane_restr0.003325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.3011080.2471895X-RAY DIFFRACTION63
1.6572-1.72350.29571190.23862202X-RAY DIFFRACTION72
1.7235-1.8020.25951110.23942488X-RAY DIFFRACTION81
1.802-1.8970.29221330.22382725X-RAY DIFFRACTION89
1.897-2.01580.21621630.20962814X-RAY DIFFRACTION92
2.0158-2.17140.24831380.22988X-RAY DIFFRACTION96
2.1714-2.38990.20931780.20372998X-RAY DIFFRACTION98
2.3899-2.73560.27471570.21593056X-RAY DIFFRACTION98
2.7356-3.44620.25421720.20953104X-RAY DIFFRACTION99
3.4462-36.26750.2191740.19853219X-RAY DIFFRACTION99

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