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- PDB-6dvu: Structure of the Monoclinic-1 (Monocl-1) Crystal Form of Human Ap... -

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Basic information

Entry
Database: PDB / ID: 6dvu
TitleStructure of the Monoclinic-1 (Monocl-1) Crystal Form of Human Apolipoprotein C1
ComponentsApolipoprotein C-I
KeywordsLIPID TRANSPORT / lipoprotein / alpha-helix / lipoprotein particles / lipid metabolism
Function / homology
Function and homology information


negative regulation of phosphatidylcholine catabolic process / negative regulation of cholesterol transport / lipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / phospholipase inhibitor activity / VLDL assembly / plasma lipoprotein particle remodeling / VLDL clearance / regulation of cholesterol transport / negative regulation of lipid metabolic process ...negative regulation of phosphatidylcholine catabolic process / negative regulation of cholesterol transport / lipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / phospholipase inhibitor activity / VLDL assembly / plasma lipoprotein particle remodeling / VLDL clearance / regulation of cholesterol transport / negative regulation of lipid metabolic process / very-low-density lipoprotein particle assembly / negative regulation of triglyceride catabolic process / chylomicron remnant clearance / negative regulation of receptor-mediated endocytosis / phosphatidylcholine-sterol O-acyltransferase activator activity / very-low-density lipoprotein particle clearance / negative regulation of fatty acid biosynthetic process / lipoprotein metabolic process / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / phosphatidylcholine binding / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol efflux / triglyceride homeostasis / triglyceride metabolic process / negative regulation of lipid catabolic process / cholesterol metabolic process / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / fatty acid binding / lipid metabolic process / endoplasmic reticulum / extracellular region
Similarity search - Function
Apolipoprotein C-I / Apolipoprotein C-I domain superfamily / Apolipoprotein C-I (ApoC-1)
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMcPherson, A. / Larson, S.B.
CitationJournal: J. Lipid Res. / Year: 2019
Title: The structure of human apolipoprotein C-1 in four different crystal forms.
Authors: McPherson, A. / Larson, S.B.
History
DepositionJun 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein C-I
B: Apolipoprotein C-I


Theoretical massNumber of molelcules
Total (without water)18,6902
Polymers18,6902
Non-polymers00
Water48627
1
A: Apolipoprotein C-I

B: Apolipoprotein C-I


Theoretical massNumber of molelcules
Total (without water)18,6902
Polymers18,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area1480 Å2
ΔGint-15 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.541, 46.739, 33.880
Angle α, β, γ (deg.)90.00, 95.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apolipoprotein C-I / ApoC-I / Apolipoprotein C1


Mass: 9344.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02654
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34 % / Description: thin monoclinic laths
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jun 15, 1992
RadiationMonochromator: Supper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0158refinement
UCSD-systemdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ROP

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
RfactorNum. reflection% reflectionSelection details
Rfree0.27626 353 4.8 %RANDOM
Rwork0.22139 ---
obs0.22426 6965 84.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.597 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å2-0.49 Å2
2---0.02 Å20 Å2
3----1.77 Å2
Refinement stepCycle: 1 / Resolution: 1.8→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 0 27 886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019876
X-RAY DIFFRACTIONr_bond_other_d0.0010.02889
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.9851160
X-RAY DIFFRACTIONr_angle_other_deg0.60832073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9565104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61824.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12415205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.166157
X-RAY DIFFRACTIONr_chiral_restr0.0550.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02918
X-RAY DIFFRACTIONr_gen_planes_other00.02173
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5392.631416
X-RAY DIFFRACTIONr_mcbond_other3.5172.622415
X-RAY DIFFRACTIONr_mcangle_it4.9713.889517
X-RAY DIFFRACTIONr_mcangle_other4.9733.898518
X-RAY DIFFRACTIONr_scbond_it5.8963.51460
X-RAY DIFFRACTIONr_scbond_other5.893.516461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9774.939643
X-RAY DIFFRACTIONr_long_range_B_refined10.75732.6021042
X-RAY DIFFRACTIONr_long_range_B_other10.75432.6081041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 16 -
Rwork0.431 370 -
obs--60.6 %

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