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- PDB-2jft: Crystal structure of the PPM Ser-Thr phosphatase MsPP from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 2jft
TitleCrystal structure of the PPM Ser-Thr phosphatase MsPP from Mycobacterium smegmatis in complex with sulfate
ComponentsSER-THR PHOSPHATASE MSPP
KeywordsHYDROLASE / PPM PHOSPHATASE / MYCOBACTERIUM / MANGANESE / SULFATE
Function / homology
Function and homology information


negative regulation of stress-activated MAPK cascade / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / negative regulation of canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of canonical NF-kappaB signal transduction / metal ion binding / cytosol
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 speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsBellinzoni, M. / Wehenkel, A. / Shepard, W. / Alzari, P.M.
CitationJournal: Structure / Year: 2007
Title: Insights Into the Mechanism of Ppm Ser/Thr Phosphatases from the Atomic Resolution Structures of a Mycobacterial Enzyme
Authors: Bellinzoni, M. / Wehenkel, A. / Shepard, W. / Alzari, P.M.
History
DepositionFeb 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5May 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
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: SER-THR PHOSPHATASE MSPP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5518
Polymers24,2781
Non-polymers2737
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.547, 84.402, 33.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-777-

HOH

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Components

#1: Protein SER-THR PHOSPHATASE MSPP


Mass: 24278.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QTQ6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST RESIDUE (GLY) IS A CLONING ARTIFACT

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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: 2.21 Å3/Da / Density % sol: 44.5 %
Crystal growpH: 8
Details: 20% PEG4000, 100 MM TRIS-HCL PH 8.0, 200 MM MGSO4, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 27, 2006 / Details: MIRRORS
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.08→20 Å / Num. obs: 93536 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.9
Reflection shellResolution: 1.08→1.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 99.1

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→6 Å / Num. parameters: 20377 / Num. restraintsaints: 25375 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1603 4650 5 %RANDOM
all0.1169 92971 --
obs0.1155 -98.7 %-
Refine analyzeNum. disordered residues: 34 / Occupancy sum hydrogen: 1634 / Occupancy sum non hydrogen: 2092.89
Refinement stepCycle: LAST / Resolution: 1.08→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 11 415 2132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0.031
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.119
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.157

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