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Yorodumi- PDB-7xqz: Drimenyl diphosphate synthase D303A from Streptomyces showdoensis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xqz | ||||||
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Title | Drimenyl diphosphate synthase D303A from Streptomyces showdoensis in complex with 2-fluorofarnesyl diphosphate (2F-FPP) and Mg2+ | ||||||
Components | SQHop_cyclase_C domain-containing protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Terpene synthases / type II TSs | ||||||
Function / homology | Function and homology information lanosterol synthase activity / triterpenoid biosynthetic process / ergosterol biosynthetic process / cholesterol biosynthetic process / lipid droplet / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces showdoensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pan, X.M. / Du, W.Y. / Yang, Q. / Zhang, B. / Dong, L.B. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xqz.cif.gz | 215.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xqz.ent.gz | 168.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xqz_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7xqz_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7xqz_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 7xqz_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xqz ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xqz | HTTPS FTP |
-Related structure data
Related structure data | 7xq4SC 7xr7C 7xraC 7xruC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) Streptomyces showdoensis (bacteria) / Gene: VO63_21045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2P2GK84 | ||||
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#2: Chemical | ChemComp-FPF / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
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: 2→46.96 Å / Num. obs: 35627 / % possible obs: 98.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.066 / Rrim(I) all: 0.125 / Net I/σ(I): 9.2 / Num. measured all: 121780 / Scaling rejects: 52 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XQ4 Resolution: 2→41.39 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.67 / 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: 84.07 Å2 / Biso mean: 23.9442 Å2 / Biso min: 8.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→41.39 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: -18.2085 Å / Origin y: -5.1138 Å / Origin z: -21.4771 Å
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Refinement TLS group | Selection details: all |