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- PDB-2cm1: Crystal structure of the catalytic domain of serine threonine pro... -

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Basic information

Entry
Database: PDB / ID: 2cm1
TitleCrystal structure of the catalytic domain of serine threonine protein phosphatase PstP in complex with 2 Manganese ions.
ComponentsSERINE THREONINE PROTEIN PHOSPHATASE PSTP
KeywordsHYDROLASE / SER/THR PROTEIN PHOSPHATASE PSTP / HYDROLASE HYPOTHETICAL PROTEIN / MYCOBACTERIUM TUBERCULOSIS
Function / homology
Function and homology information


protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphoprotein phosphatase activity / membrane => GO:0016020 / peptidoglycan-based cell wall / manganese ion binding / regulation of DNA-templated transcription / magnesium ion binding / signal transduction / metal ion binding ...protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphoprotein phosphatase activity / membrane => GO:0016020 / peptidoglycan-based cell wall / manganese ion binding / regulation of DNA-templated transcription / magnesium ion binding / signal transduction / metal ion binding / membrane / plasma membrane
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
: / Serine/threonine protein phosphatase PstP / Serine/threonine protein phosphatase PstP
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWehenkel, A. / Villarino, A. / Bellinzoni, M. / 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 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 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 / 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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: SERINE THREONINE PROTEIN PHOSPHATASE PSTP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8364
Polymers27,6341
Non-polymers2023
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.142, 69.142, 89.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SERINE THREONINE PROTEIN PHOSPHATASE PSTP


Mass: 27633.984 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-240
Source method: isolated from a genetically manipulated source
Details: 2 MANGANESE IONS BOUND IN THE ACTIVE SITE / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P71588, UniProt: P9WHW5*PLUS, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Description: REJECTION CRITERIA FOR RESOLUTION CUTOFF AT MERGING R VALUE BELOW 0.4
Crystal growDetails: 14% PEG 8000, 50MM KH2PO4 PH6.5, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2005 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 15969 / % possible obs: 92.8 % / Observed criterion σ(I): 3.96 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.67
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.96 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TXO

1txo


Resolution: 2→59.87 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.674 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 799 5 %RANDOM
Rwork0.197 ---
obs0.199 15173 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2→59.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 8 143 1818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211703
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9862309
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4315230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56623.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72415269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5211515
X-RAY DIFFRACTIONr_chiral_restr0.1030.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021269
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.2827
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21172
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1511.51168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84121800
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7313581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4084.5508
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 60
Rwork0.253 1148

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