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Yorodumi- PDB-2cm1: Crystal structure of the catalytic domain of serine threonine pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cm1 | ||||||
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Title | Crystal structure of the catalytic domain of serine threonine protein phosphatase PstP in complex with 2 Manganese ions. | ||||||
Components | SERINE THREONINE PROTEIN PHOSPHATASE PSTP | ||||||
Keywords | HYDROLASE / SER/THR PROTEIN PHOSPHATASE PSTP / HYDROLASE HYPOTHETICAL PROTEIN / MYCOBACTERIUM TUBERCULOSIS | ||||||
Function / homology | Function and homology information negative regulation of catalytic activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of catalytic activity / negative regulation of DNA binding / phosphoprotein phosphatase activity / peptidoglycan-based cell wall / protein dephosphorylation / negative regulation of protein kinase activity ...negative regulation of catalytic activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of catalytic activity / negative regulation of DNA binding / phosphoprotein phosphatase activity / peptidoglycan-based cell wall / protein dephosphorylation / negative regulation of protein kinase activity / manganese ion binding / membrane => GO:0016020 / magnesium ion binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wehenkel, A. / Villarino, A. / Bellinzoni, M. / Alzari, P.M. | ||||||
Citation | Journal: 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 |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cm1.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cm1.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/2cm1 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/2cm1 | HTTPS FTP |
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-Related structure data
Related structure data | 2v06C 1txoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | 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 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % Description: REJECTION CRITERIA FOR RESOLUTION CUTOFF AT MERGING R VALUE BELOW 0.4 |
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Crystal grow | Details: 14% PEG 8000, 50MM KH2PO4 PH6.5, 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2005 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.96 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2→59.87 Å
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