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- PDB-2j86: Structural analysis of the PP2C Family Phosphatase tPphA of Therm... -

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Basic information

Entry
Database: PDB / ID: 2j86
TitleStructural analysis of the PP2C Family Phosphatase tPphA of Thermosynechococcus elongatus
ComponentsPROTEIN SERINE-THREONINE PHOSPHATASE
KeywordsHYDROLASE / THERMOSYNECHOCOCCUS ELONGATUS BP-1 / PPHA / PP2C / CYANOBACTERIA / INTRINSIC DISORDER
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: 3.05 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 19, 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 1.3Dec 13, 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
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.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.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
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
B: PROTEIN SERINE-THREONINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6208
Polymers53,4742
Non-polymers1466
Water23413
1
A: PROTEIN SERINE-THREONINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8104
Polymers26,7371
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN SERINE-THREONINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8104
Polymers26,7371
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.290, 113.290, 88.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROTEIN SERINE-THREONINE PHOSPHATASE / TPPHA


Mass: 26736.975 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.84 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growDetails: 0.1 M TRIS PH 7.0, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 89.5 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97629
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 3.05→25 Å / Num. obs: 11417 / % possible obs: 99.9 % / Observed criterion σ(I): 5.6 / Redundancy: 1.86 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.72
Reflection shellResolution: 3.05→3.15 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.22 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J82

2j82


Resolution: 3.05→25 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 591 5.2 %RANDOM
Rwork0.2402 ---
obs0.2402 11417 99.9 %-
Solvent computationBsol: 26.5066 Å2 / ksol: 0.286674 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.66 Å20 Å20 Å2
2---8.66 Å20 Å2
3---17.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5199 Å0.3987 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4597 Å0.4534 Å
Refinement stepCycle: LAST / Resolution: 3.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 6 13 3453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00742
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.30344
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.83527
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81349
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMCOOT15_SLS.MTF
X-RAY DIFFRACTION2ION.PARAMCOOT15_SLS.MTF
X-RAY DIFFRACTION3WATER_REP.PARAMCOOT15_SLS.MTF

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