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Yorodumi- PDB-5e8k: Crystal structure of polyprenyl pyrophosphate synthase 2 from Ara... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e8k | ||||||
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Title | Crystal structure of polyprenyl pyrophosphate synthase 2 from Arabidopsis thaliana | ||||||
Components | Geranylgeranyl pyrophosphate synthase 10, mitochondrial | ||||||
Keywords | TRANSFERASE / AtPPPS2 | ||||||
Function / homology | Function and homology information carotenoid biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity ...carotenoid biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.028 Å | ||||||
Authors | Wang, C. / Chen, Q. / Fan, D. / Li, J. / Wang, G. / Zhang, P. | ||||||
Citation | Journal: Mol Plant / Year: 2016 Title: Structural Analyses of Short-Chain Prenyltransferases Identify an Evolutionarily Conserved GFPPS Clade in Brassicaceae Plants. Authors: Wang, C. / Chen, Q. / Fan, D. / Li, J. / Wang, G. / Zhang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e8k.cif.gz | 215.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e8k.ent.gz | 177.7 KB | Display | PDB format |
PDBx/mmJSON format | 5e8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/5e8k ftp://data.pdbj.org/pub/pdb/validation_reports/e8/5e8k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34365.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g20160, MAL21.19 / Production host: Escherichia coli (E. coli) References: UniProt: Q9LJY2, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 5% isopropanol, 8% PEG 4000, pH5.9 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 16306 / % possible obs: 99.7 % / Redundancy: 4.9 % / Net I/σ(I): 10.9 |
-Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3.028→50 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.028→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -44.436 Å / Origin y: -16.4051 Å / Origin z: 30.263 Å
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Refinement TLS group | Selection details: all |