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- PDB-7pax: Structure of the human heterotetrameric cis-prenyltransferase com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pax | ||||||||||||||||||||||||
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Title | Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, FsPP and IPP | ||||||||||||||||||||||||
![]() | (Dehydrodolichyl diphosphate synthase complex subunit ...) x 2 | ||||||||||||||||||||||||
![]() | TRANSFERASE / DHDDS / NgBR / hcit / cis-prenyltransferase / dolichol | ||||||||||||||||||||||||
Function / homology | ![]() protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / dolichyl diphosphate biosynthetic process / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process ...protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / dolichyl diphosphate biosynthetic process / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / vascular endothelial growth factor signaling pathway / protein glycosylation / positive regulation of blood vessel endothelial cell migration / lipid droplet / positive regulation of nitric-oxide synthase activity / cholesterol homeostasis / angiogenesis / cell differentiation / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Giladi, M. / Lisnyansky Bar-El, M. / Haitin, Y. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for long-chain isoprenoid synthesis by cis -prenyltransferases. Authors: Giladi, M. / Lisnyansky Bar-El, M. / Vankova, P. / Ferofontov, A. / Melvin, E. / Alkaderi, S. / Kavan, D. / Redko, B. / Haimov, E. / Wiener, R. / Man, P. / Haitin, 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 | ![]() | 226.5 KB | Display | ![]() |
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PDB format | ![]() | 180.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7payC ![]() 7pb0C ![]() 7pb1C ![]() 6z1nS S: Starting model for refinement C: citing same article ( |
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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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Dehydrodolichyl diphosphate synthase complex subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 39201.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q86SQ9, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] |
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#2: Protein | Mass: 24211.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96E22, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] |
-Non-polymers , 4 types, 82 molecules ![](data/chem/img/IPE.gif)
![](data/chem/img/FPS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FPS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IPE / |
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#4: Chemical | ChemComp-FPS / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M NaCl, 0.1 M MES, 33% w/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2→46 Å / Num. obs: 47371 / % possible obs: 96.3 % / Redundancy: 20.9 % / CC1/2: 1 / Rrim(I) all: 0.066 / Net I/σ(I): 22.94 |
Reflection shell | Resolution: 2→2.12 Å / Mean I/σ(I) obs: 1.23 / Num. unique obs: 7888 / CC1/2: 0.696 / Rrim(I) all: 2.005 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Z1N Resolution: 2→41.134 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.92 / 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: 2→41.134 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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