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- PDB-7xra: Drimenyl diphosphate synthase D303A from Streptomyces showdoensis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xra | ||||||
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Title | Drimenyl diphosphate synthase D303A from Streptomyces showdoensis in complex with farnesyl diphosphate (FPP) and Mg2+ | ||||||
![]() | SQHop_cyclase_C domain-containing protein | ||||||
![]() | BIOSYNTHETIC PROTEIN / Terpene synthases / type II TSs | ||||||
Function / homology | ![]() lanosterol synthase activity / triterpenoid biosynthetic process / ergosterol biosynthetic process / cholesterol biosynthetic process / lipid droplet / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pan, X.M. / Du, W.Y. / Yang, Q. / Zhang, B. / Dong, L.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery, Structure, and Mechanism of a Class II Sesquiterpene Cyclase. Authors: Pan, X. / Du, W. / Zhang, X. / Lin, X. / Li, F.R. / Yang, Q. / Wang, H. / Rudolf, J.D. / Zhang, B. / Dong, L.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.5 KB | Display | ![]() |
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PDB format | ![]() | 166.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xq4C ![]() 7xqzSC ![]() 7xr7C ![]() 7xruC C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55044.164 Da / Num. of mol.: 1 / Mutation: D303A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-FPP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 15, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→60.02 Å / Num. obs: 38605 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.84 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.132 / Net I/σ(I): 7.7 / Num. measured all: 129439 / Scaling rejects: 16 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7XQZ Resolution: 1.95→30.42 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.95 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.97 Å2 / Biso mean: 22.8243 Å2 / Biso min: 8.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→30.42 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -18.0762 Å / Origin y: -5.203 Å / Origin z: -21.3925 Å
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Refinement TLS group | Selection details: all |