+Open data
-Basic information
Entry | Database: PDB / ID: 1mvl | ||||||
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Title | PPC decarboxylase mutant C175S | ||||||
Components | PPC decarboxylase AtHAL3a | ||||||
Keywords | LYASE / Flavoprotein / PPC decarboxylase / active site mutant C175S | ||||||
Function / homology | Function and homology information phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / hyperosmotic salinity response / coenzyme A biosynthetic process / FMN binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Steinbacher, S. / Hernandez-Acosta, P. / Bieseler, B. / Blaesse, M. / Huber, R. / Culianez-Macia, F.A. / Kupke, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of the Plant PPC Decarboxylase AtHAL3a Complexed with an Ene-thiol Reaction Intermediate Authors: Steinbacher, S. / Hernandez-Acosta, P. / Bieseler, B. / Blaesse, M. / Huber, R. / Culianez-Macia, F.A. / Kupke, T. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Arabidopsis thaliana flavoprotein AtHAL3a catalyzes the decarboxylation of 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a key step in coenzyme A biosynthesis Authors: Kupke, T. / Hernandez-Acosta, P. / Steinbacher, S. / Culianez-Macia, F.A. #2: Journal: J.Biol.Chem. / Year: 2002 Title: Molecular characterization of the Arabidopsis thaliana flavoprotein AtHAL3a reveals the general reaction mechanism of 4'-phosphopantothenoylcysteine decarboxylases Authors: Hernandez-Acosta, P. / Schmid, D.G. / Jung, G. / Culianez-Macia, F.A. / Kupke, T. #3: Journal: Plant J. / Year: 1999 Title: Arabidopsis thaliana AtHal3: a flavoprotein related to salt and osmotic tolerance and plant growth Authors: Espinosa-Ruiz, A. / Belles, J.M. / Serrano, R. / Culianez-Macia, F.A. #4: Journal: Structure / Year: 2000 Title: The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction Authors: Albert, A. / Martinez-Ripoll, M. / Espinosa-Ruiz, A. / Yenush, L. / Culianez-Macia, F.A. / Serrano, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mvl.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mvl.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mvl_validation.pdf.gz | 771.5 KB | Display | wwPDB validaton report |
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Full document | 1mvl_full_validation.pdf.gz | 773.5 KB | Display | |
Data in XML | 1mvl_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1mvl_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/1mvl ftp://data.pdbj.org/pub/pdb/validation_reports/mv/1mvl | HTTPS FTP |
-Related structure data
Related structure data | 1mvnC 1e20S 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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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the three-fold axis |
-Components
#1: Protein | Mass: 23364.775 Da / Num. of mol.: 1 / Mutation: C175S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) References: UniProt: Q9SWE5, phosphopantothenoylcysteine decarboxylase |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.22 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: ammonium sulphate, imidazole, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2002 / Details: mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 15995 / Num. obs: 15995 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.22 / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1E20 Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→20 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.169 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |