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- PDB-8hdl: Crystal structure of ASFV trans geranylgeranyl diphosphate syntha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hdl | ||||||
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Title | Crystal structure of ASFV trans geranylgeranyl diphosphate synthase B318L | ||||||
![]() | Trans-prenyltransferase | ||||||
![]() | TRANSFERASE / ASFV | ||||||
Function / homology | ![]() geranylfarnesyl diphosphate synthase activity / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyltranstransferase activity / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity ...geranylfarnesyl diphosphate synthase activity / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyltranstransferase activity / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / host cell endoplasmic reticulum / host cell membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, H.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Exploring AlphaFold2's Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein. Authors: Zhao, H. / Zhang, H. / She, Z. / Gao, Z. / Wang, Q. / Geng, Z. / Dong, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.6 KB | Display | ![]() |
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PDB format | ![]() | 91.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 32329.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Ba71V-074, B318L / Production host: ![]() ![]() References: UniProt: Q65164, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.57 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4.3 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.198→48.21 Å / Num. obs: 6579 / % possible obs: 99.7 % / Redundancy: 31.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.297 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3.2→3.28 Å / Num. unique obs: 472 / CC1/2: 0.718 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold2 Resolution: 3.198→48.21 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.34 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.198→48.21 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.0849 Å / Origin y: 14.7343 Å / Origin z: -14.278 Å
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Refinement TLS group | Selection details: all |