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- PDB-6dz6: Structure of the Orthorhombic (Orthrhmb) Crystal Form of Human Ap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dz6 | ||||||
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Title | Structure of the Orthorhombic (Orthrhmb) Crystal Form of Human Apolipoprotein C1 | ||||||
![]() | Apolipoprotein C-I | ||||||
![]() | LIPID BINDING PROTEIN / lipoprotein particles / lipids / alpha helix | ||||||
Function / homology | ![]() negative regulation of phosphatidylcholine catabolic process / VLDL clearance / VLDL assembly / lipase inhibitor activity / negative regulation of cholesterol transport / phospholipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / negative regulation of lipoprotein lipase activity / plasma lipoprotein particle remodeling / regulation of cholesterol transport ...negative regulation of phosphatidylcholine catabolic process / VLDL clearance / VLDL assembly / lipase inhibitor activity / negative regulation of cholesterol transport / phospholipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / negative regulation of lipoprotein lipase activity / plasma lipoprotein particle remodeling / regulation of cholesterol transport / very-low-density lipoprotein particle assembly / negative regulation of lipid metabolic process / negative regulation of receptor-mediated endocytosis / chylomicron remnant clearance / very-low-density lipoprotein particle clearance / negative regulation of fatty acid biosynthetic process / phosphatidylcholine-sterol O-acyltransferase activator activity / lipoprotein metabolic process / chylomicron / phosphatidylcholine binding / high-density lipoprotein particle remodeling / phospholipid efflux / very-low-density lipoprotein particle / high-density lipoprotein particle / cholesterol efflux / triglyceride metabolic process / negative regulation of lipid catabolic process / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cholesterol metabolic process / fatty acid binding / lipid metabolic process / endoplasmic reticulum / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | McPherson, A. | ||||||
![]() | ![]() Title: The structure of human apolipoprotein C-1 in four different crystal forms. Authors: McPherson, A. / Larson, S.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.7 KB | Display | ![]() |
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PDB format | ![]() | 22.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.6 KB | Display | ![]() |
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Full document | ![]() | 421.2 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 5 - 53 / Label seq-ID: 31 - 79
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Components
#1: Protein | Mass: 9344.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 30.2 % / Description: rectangular blocks |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 16% MPD - 18% MPD / PH range: 5.5-7.0 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Aug 15, 1992 |
Radiation | Monochromator: Supper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→42 Å / Num. obs: 2687 / % possible obs: 91.8 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.08 / Rrim(I) all: 0.18 / Rsym value: 0.169 / Net I/av σ(I): 5.5 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 180 / CC1/2: 0.733 / Rpim(I) all: 0.369 / Rrim(I) all: 0.619 / Rsym value: 0.491 / % possible all: 56.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.741 Å2
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Refinement step | Cycle: 1 / Resolution: 3→42 Å
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Refine LS restraints |
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