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Yorodumi- PDB-3pyb: Crystal structure of ent-copalyl diphosphate synthase from Arabid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pyb | ||||||
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Title | Crystal structure of ent-copalyl diphosphate synthase from Arabidopsis thaliana in complex with 13-aza-13,14-dihydrocopalyl diphosphate | ||||||
Components | Ent-copalyl diphosphate synthase, chloroplastic | ||||||
Keywords | ISOMERASE / class I and II terpene cyclase fold / class II diterpene cyclase / DXXDD motif / gibberellin biosynthesis / Biosynthesis of ent-copalyl diphosphate | ||||||
Function / homology | Function and homology information ent-copalyl diphosphate synthase / ent-copalyl diphosphate synthase activity / gibberellin biosynthetic process / gibberellic acid mediated signaling pathway / terpene synthase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.759 Å | ||||||
Authors | Koksal, M. / Christianson, D.W. | ||||||
Citation | Journal: To be Published Title: Structure of ent-Copalyl Diphosphate Synthase from Arabidopsis thaliana, a Protonation-Dependent Diterpene Cyclase Authors: Koksal, M. / Hu, H. / Coates, R.M. / Peters, R.J. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pyb.cif.gz | 429.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pyb.ent.gz | 352 KB | Display | PDB format |
PDBx/mmJSON format | 3pyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pyb_validation.pdf.gz | 759.3 KB | Display | wwPDB validaton report |
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Full document | 3pyb_full_validation.pdf.gz | 807.7 KB | Display | |
Data in XML | 3pyb_validation.xml.gz | 75.8 KB | Display | |
Data in CIF | 3pyb_validation.cif.gz | 101.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/3pyb ftp://data.pdbj.org/pub/pdb/validation_reports/py/3pyb | HTTPS FTP |
-Related structure data
Related structure data | 3pyaSC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 84840.266 Da / Num. of mol.: 3 / Fragment: ent-Copalyl Diphosphate Synthase Source method: isolated from a genetically manipulated source Details: vector: pET22bTV is a derivative of pET22b / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g02780, GA1, T5J8.9, TPSGA1 / Plasmid: pET22bCV / Production host: Escherichia coli (E. coli) / Strain (production host): OverExpress C41 (DE3) References: UniProt: Q38802, ent-copalyl diphosphate synthase #2: Chemical | ChemComp-A3C / | #3: Chemical | ChemComp-1PE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 100 mM sodium citrate (pH 5.4), 30 % polyethylene glycol 400, 200 mM KH2PO4, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2010 / Details: Kirpatrick Baez focusing mirrors |
Radiation | Monochromator: Si(111) double crystal monochromator (Kohzu HLD8-24 Monochromator) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 67547 / Num. obs: 67547 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.227 / Num. unique all: 6022 / Rsym value: 0.768 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PYA Resolution: 2.759→44.519 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.08 / 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 / Bsol: 37.336 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.759→44.519 Å
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Refine LS restraints |
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LS refinement shell |
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