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Yorodumi- PDB-7pb0: Structure of the human heterotetrameric cis-prenyltransferase com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pb0 | ||||||||||||||||||||||||
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Title | Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, GGsPP and IsPP | ||||||||||||||||||||||||
Components | (Dehydrodolichyl diphosphate synthase complex subunit ...) x 2 | ||||||||||||||||||||||||
Keywords | TRANSFERASE / DHDDS / NgBR / hcit / cis-prenyltransferase / dolichol | ||||||||||||||||||||||||
Function / homology | Function and homology information dolichyl diphosphate biosynthetic process / protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process ...dolichyl diphosphate biosynthetic process / protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / vascular endothelial growth factor signaling pathway / protein glycosylation / positive regulation of blood vessel endothelial cell migration / cholesterol homeostasis / positive regulation of nitric-oxide synthase activity / angiogenesis / cell differentiation / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å | ||||||||||||||||||||||||
Authors | Giladi, M. / Lisnyansky Bar-El, M. / Haitin, Y. | ||||||||||||||||||||||||
Funding support | Israel, 7items
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Citation | Journal: Sci Adv / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pb0.cif.gz | 222.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pb0.ent.gz | 175.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pb0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7pb0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7pb0_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 7pb0_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/7pb0 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/7pb0 | HTTPS FTP |
-Related structure data
Related structure data | 7paxC 7payC 7pb1C 6z1nS C: citing same article (ref.) S: Starting model for refinement |
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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
-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.) Homo sapiens (human) / Gene: DHDDS, HDS / Production host: Escherichia coli (E. coli) 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.) Homo sapiens (human) / Gene: NUS1, C6orf68, NGBR / Production host: Escherichia coli (E. coli) References: UniProt: Q96E22, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] |
-Non-polymers , 4 types, 133 molecules
#3: Chemical | ChemComp-ISY / |
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#4: Chemical | ChemComp-GGS / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.16 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M KCl, 0.1 M MES, 36% w/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.2 Å / Num. obs: 32739 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.995 / Rrim(I) all: 0.14 / Net I/σ(I): 8.23 |
Reflection shell | Resolution: 2.3→2.44 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5106 / CC1/2: 0.547 / Rrim(I) all: 1.112 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z1N Resolution: 2.301→46.198 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25 / 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: 2.301→46.198 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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