+Open data
-Basic information
Entry | Database: PDB / ID: 6u8z | |||||||||
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Title | Crystal Structure of Catalytic Domain of Human Phospholipase D1 | |||||||||
Components | Phospholipase D1,Phospholipase D1 | |||||||||
Keywords | HYDROLASE / Phospholipase D1 / PLD / phosphohistidine / PIP2 binding | |||||||||
Function / homology | Function and homology information : / Synthesis of PG / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D activity / phospholipid catabolic process / cholinergic synapse ...: / Synthesis of PG / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D activity / phospholipid catabolic process / cholinergic synapse / regulation of synaptic vesicle cycle / regulation of vesicle-mediated transport / small GTPase-mediated signal transduction / tertiary granule membrane / CDC42 GTPase cycle / endocytic vesicle / RHOG GTPase cycle / RHOA GTPase cycle / Role of phospholipids in phagocytosis / specific granule membrane / RAC1 GTPase cycle / phosphatidylinositol binding / positive regulation of translation / chemotaxis / late endosome membrane / Ras protein signal transduction / endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.799 Å | |||||||||
Authors | Bowling, F.Z. / Airola, M.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Crystal structure of human PLD1 provides insight into activation by PI(4,5)P2and RhoA. Authors: Bowling, F.Z. / Salazar, C.M. / Bell, J.A. / Huq, T.S. / Frohman, M.A. / Airola, M.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u8z.cif.gz | 372.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u8z.ent.gz | 320.8 KB | Display | PDB format |
PDBx/mmJSON format | 6u8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u8z ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u8z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 69671.414 Da / Num. of mol.: 1 / Fragment: UNP residues 330-500,643-1074 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLD1 / Plasmid: pFastbac Htb / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13393, phospholipase D |
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#2: Chemical | ChemComp-PO3 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 0.2 M ammonium citrate, 15% PEG3350, pH 5.3 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.97933 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.799→79.88 Å / Num. obs: 64302 / % possible obs: 99 % / Redundancy: 8.7 % / Biso Wilson estimate: 30.221 Å2 / Rpim(I) all: 0.053 / Rrim(I) all: 0.158 / Net I/σ(I): 7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.799→54.759 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.43 Å2 / Biso mean: 49.9468 Å2 / Biso min: 19.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.799→54.759 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 32.897 Å / Origin y: 70.85 Å / Origin z: 103.093 Å
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Refinement TLS group |
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