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- PDB-6dvu: Structure of the Monoclinic-1 (Monocl-1) Crystal Form of Human Ap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dvu | ||||||
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Title | Structure of the Monoclinic-1 (Monocl-1) Crystal Form of Human Apolipoprotein C1 | ||||||
![]() | Apolipoprotein C-I | ||||||
![]() | LIPID TRANSPORT / lipoprotein / alpha-helix / lipoprotein particles / lipid metabolism | ||||||
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 / chylomicron remnant clearance / negative regulation of receptor-mediated endocytosis / 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. / Larson, S.B. | ||||||
![]() | ![]() 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 | ![]() | 35.1 KB | Display | ![]() |
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PDB format | ![]() | 23 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 432.2 KB | Display | ![]() |
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Full document | ![]() | 432.8 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dxrC ![]() 6dz6C ![]() 6nf3C ![]() 1ropS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 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: 1.87 Å3/Da / Density % sol: 34 % / Description: thin monoclinic laths |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Crystallized in Cryschem sitting drop plates with reservoirs of 16%-18% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium acetate and 0.25% octyl-beta-s-1-thioglucopyanoside. The drops were ...Details: Crystallized in Cryschem sitting drop plates with reservoirs of 16%-18% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium acetate and 0.25% octyl-beta-s-1-thioglucopyanoside. The drops were composed of equal amounts of 8 mg/ml protein in 0.02 ammonium bicarbonate and reservoir. PH range: 5.0 7.0 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jun 15, 1992 |
Radiation | Monochromator: Supper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35 Å / Num. obs: 7315 / % possible obs: 85.2 % / Redundancy: 7.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.055 / Rrim(I) all: 0.114 / Rsym value: 0.094 / Net I/av σ(I): 6.7 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.8→1.95 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 613 / CC1/2: 0.64 / Rpim(I) all: 0.315 / Rrim(I) all: 0.721 / Rsym value: 0.457 / % possible all: 76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ROP Resolution: 1.8→33 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.135 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.597 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→33 Å
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Refine LS restraints |
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