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Yorodumi- PDB-2pmp: Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pmp | ||||||
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Title | Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid biosynthetic pathway of Arabidopsis thaliana | ||||||
Components | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | LYASE / Plant enzymes / Arabidopsis thaliana / MEP pathway / Isoprenoid-binding proteins / CMP / Zinc ions | ||||||
Function / homology | Function and homology information carotenoid biosynthetic process / chlorophyll biosynthetic process / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / chloroplast stroma / chloroplast / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Calisto, B.M. / Perez-Gil, J. / Querol-Audi, J. / Fita, I. / Imperial, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Biosynthesis of isoprenoids in plants: Structure of the 2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase from Arabidopsis thaliana. Comparison with the bacterial enzymes. Authors: Calisto, B.M. / Perez-Gil, J. / Bergua, M. / Querol-Audi, J. / Fita, I. / Imperial, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pmp.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pmp.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/2pmp ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pmp | HTTPS FTP |
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-Related structure data
Related structure data | 1gx1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 operations: z, x, y and y, z, x. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17349.080 Da / Num. of mol.: 1 / Fragment: IspF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Ecotype Columbia 0 / Gene: ISPF / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) [pLysS] References: UniProt: Q9CAK8, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 5 types, 72 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-C5P / |
#6: 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: 3.01 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 18% PEG3350, 100mM MES, 200mM Ammonium Dihydrogen Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0358 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0358 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.6 Å / Num. all: 9624 / Num. obs: 9624 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.6 % / Biso Wilson estimate: 56 Å2 / Rsym value: 0.057 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.3 % / Num. unique all: 602 / Rsym value: 0.422 / % possible all: 89.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GX1 Resolution: 2.3→19.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.939 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.272 / ESU R Free: 0.224 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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