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- PDB-2v06: Crystal structure of the PPM Ser-Thr phosphatase MsPP from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 2v06
TitleCrystal structure of the PPM Ser-Thr phosphatase MsPP from Mycobacterium smegmatis at pH 5.5
ComponentsSER-THR PHOSPHATASE MSPP
KeywordsHYDROLASE / PP2C-LIKE PHOSPHATASE / METAL BINDING / MYCOBACTERIUM / REGULATORY PROTEIN
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 / OTHER / Resolution: 1.05 Å
AuthorsWehenkel, A. / Bellinzoni, M. / Schaeffer, F. / Villarino, A. / Alzari, P.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and Binding Studies of the Three-Metal Center in Two Mycobacterial Ppm Ser/Thr Protein Phosphatases.
Authors: Wehenkel, A. / Bellinzoni, M. / Schaeffer, F. / Villarino, A. / Alzari, P.M.
History
DepositionMay 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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.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: SER-THR PHOSPHATASE MSPP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3865
Polymers24,2781
Non-polymers1084
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.718, 83.596, 33.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: MC2155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QTQ6, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE GLY0 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: 2.1 Å3/Da / Density % sol: 40.9 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 3, 2006 / Details: MIRRORS
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.05→15 Å / Num. obs: 97914 / % possible obs: 98.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 11.3
Reflection shellResolution: 1.05→1.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.05→6 Å / Num. parameters: 20542 / Num. restraintsaints: 26496 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 4873 5 %RANDOM
all0.1328 97463 --
obs0.1314 -98.8 %-
Refine analyzeNum. disordered residues: 81 / Occupancy sum hydrogen: 1634 / Occupancy sum non hydrogen: 2062.17
Refinement stepCycle: LAST / Resolution: 1.05→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 4 387 2097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.046
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0.1

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