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Yorodumi- PDB-3g4f: Crystal Structure of (+)- -Cadinene Synthase from Gossypium arbor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g4f | ||||||
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Title | Crystal Structure of (+)- -Cadinene Synthase from Gossypium arboreum in complex with 2-fluorofarnesyl diphosphate | ||||||
Components | (+)-delta-cadinene synthase isozyme XC1 | ||||||
Keywords | LYASE / Cyclase / Magnesium / Metal-binding | ||||||
Function / homology | Function and homology information (+)-delta-cadinene synthase / (+)-delta-cadinene synthase activity / diterpenoid biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Gossypium arboreum (tree cotton) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å | ||||||
Authors | Gennadios, H.A. / Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Crystal structure of (+)-delta-cadinene synthase from Gossypium arboreum and evolutionary divergence of metal binding motifs for catalysis. Authors: Gennadios, H.A. / Gonzalez, V. / Di Costanzo, L. / Li, A. / Yu, F. / Miller, D.J. / Allemann, R.K. / 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 | 3g4f.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g4f.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g4f_validation.pdf.gz | 983.4 KB | Display | wwPDB validaton report |
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Full document | 3g4f_full_validation.pdf.gz | 1021.8 KB | Display | |
Data in XML | 3g4f_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 3g4f_validation.cif.gz | 59.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/3g4f ftp://data.pdbj.org/pub/pdb/validation_reports/g4/3g4f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64217.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gossypium arboreum (tree cotton) / Production host: Escherichia coli (E. coli) / References: UniProt: Q39761, (+)-delta-cadinene synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: 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: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: crystals of unliganded DCS were gradually transferred to a stabilizing solution containing 100 mM Tris (pH 7.5), 200 mM Li2SO4, 17-19% PEG 4000, 2 mM 2F-FPP and allowed to soak for 16 hours. ...Details: crystals of unliganded DCS were gradually transferred to a stabilizing solution containing 100 mM Tris (pH 7.5), 200 mM Li2SO4, 17-19% PEG 4000, 2 mM 2F-FPP and allowed to soak for 16 hours. Crystals were slowly cryoprotected with stabilizing solution containing 2 mM MnCl2 and 25% glycerol and then flash cooled with liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.651→50 Å / Num. obs: 38457 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.651→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.487 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The unliganded structure Resolution: 2.651→47.698 Å / SU ML: 0.83 / σ(F): 1.35 / Phase error: 33.06 / 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: 42.288 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.651→47.698 Å
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Refine LS restraints |
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LS refinement shell |
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