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- PDB-2j82: Structural analysis of the PP2C Family Phosphatase tPphA from The... -

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Basic information

Entry
Database: PDB / ID: 2j82
TitleStructural analysis of the PP2C Family Phosphatase tPphA from Thermosynechococcus elongatus
ComponentsPROTEIN SERINE-THREONINE 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 / MAD / Resolution: 1.28 Å
AuthorsSchlicker, C. / Kloft, N. / Forchhammer, K. / Becker, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Analysis of the Pp2C Phosphatase Tppha from Thermosynechococcus Elongatus: A Flexible Flap Subdomain Controls Access to the Catalytic Site.
Authors: Schlicker, C. / Fokina, O. / Kloft, N. / Grune, T. / Becker, S. / Sheldrick, G.M. / Forchhammer, K.
History
DepositionOct 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_source
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN SERINE-THREONINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8665
Polymers26,7371
Non-polymers1294
Water2,450136
1
A: PROTEIN SERINE-THREONINE PHOSPHATASE
hetero molecules

A: PROTEIN SERINE-THREONINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,73110
Polymers53,4742
Non-polymers2588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1550 Å2
ΔGint-1.8 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.216, 151.799, 82.505
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-2061-

HOH

21A-2089-

HOH

31A-2111-

HOH

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Components

#1: Protein PROTEIN SERINE-THREONINE PHOSPHATASE / TPPHA


Mass: 26736.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Plasmid: PET32A-TPPHA-1-240 / 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.: 136 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growDetails: 0.2 M CACL2, 0.1 M HEPES PH 8.0, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.95,0.9796,1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97961
31.051
ReflectionResolution: 1.28→75.81 Å / Num. obs: 61884 / % possible obs: 99.2 % / Observed criterion σ(I): 2.1 / Redundancy: 0.99 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 25.01
Reflection shellResolution: 1.28→1.37 Å / Redundancy: 0.98 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.32 / % possible all: 98

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.28→75.81 Å / Num. restraintsaints: 20937 / Cross valid method: THROUGHOUT / σ(F): 2.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 3619 5 %RANDOM
all0.1653 61884 --
obs0.1633 -99.2 %-
Refinement stepCycle: LAST / Resolution: 1.28→75.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 4 136 1794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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