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- PDB-3g4d: Crystal Structure of (+)-delta-Cadinene Synthase from Gossypium a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g4d | ||||||
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Title | Crystal Structure of (+)-delta-Cadinene Synthase from Gossypium arboreum and Evolutionary Divergence of Metal Binding Motifs for Catalysis | ||||||
![]() | (+)-delta-cadinene synthase isozyme XC1 | ||||||
![]() | LYASE / cyclase / Magnesium / Metal-binding | ||||||
Function / homology | ![]() (+)-delta-cadinene synthase / (+)-delta-cadinene synthase activity / diterpenoid biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gennadios, H.A. / Di Costanzo, L. / Miller, D.J. / Allemann, R.K. / Christianson, D.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.9 KB | Display | ![]() |
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PDB format | ![]() | 182.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3g4fC ![]() 5eatS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 8 Details: drop containing 5 L protein solution (10 mg/mL DCS, 20 mM Tris (pH 8.0), 2 mM MgCl2, 5 mM BME) and 5 L precipitant solution (100 mM Tris (pH 7.5), 200 mM Li2SO4, 15-17% polyethylene glycol ...Details: drop containing 5 L protein solution (10 mg/mL DCS, 20 mM Tris (pH 8.0), 2 mM MgCl2, 5 mM BME) and 5 L precipitant solution (100 mM Tris (pH 7.5), 200 mM Li2SO4, 15-17% polyethylene glycol (PEG) 4000, 100 mM BaCl2 2H2O) was suspended over a reservoir of 600 L precipitant solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 51262 / Num. obs: 51262 / % possible obs: 99.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 4.65 / Num. unique all: 5144 / Rsym value: 0.525 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Nicotiana tabacum 5-epi aristolochene synthase (PDB ENTRY 5EAT) Resolution: 2.403→47.698 Å / SU ML: 0.36 / σ(F): 1.34 / 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: 71.95 Å2 / ksol: 0.345 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.403→47.698 Å
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Refine LS restraints |
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LS refinement shell |
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