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- PDB-6dxr: Structure of the Monoclinic-2 (Monocl-2) Crystal Form of Human Ap... -

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Basic information

Entry
Database: PDB / ID: 6dxr
TitleStructure of the Monoclinic-2 (Monocl-2) Crystal Form of Human Apolipoprotein C1
ComponentsApolipoprotein C-I
KeywordsLIPID BINDING PROTEIN / lipoprotein particles / lipids / alpha helix
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 / regulation of cholesterol transport / VLDL clearance / 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 / regulation of cholesterol transport / VLDL clearance / 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 / negative regulation of fatty acid biosynthetic process / very-low-density lipoprotein particle clearance / 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: 2 Å
AuthorsMcPherson, A.
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 29, 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 / _citation.year
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9264
Polymers18,6902
Non-polymers2362
Water43224
1
A: Apolipoprotein C-I
hetero molecules

B: Apolipoprotein C-I


Theoretical massNumber of molelcules
Total (without water)18,9264
Polymers18,6902
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area1880 Å2
ΔGint-26 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.889, 46.472, 34.088
Angle α, β, γ (deg.)90.00, 94.14, 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.64 Å3/Da / Density % sol: 25 % / Description: thin laths
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG / PH range: 5.5 -6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 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: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→34 Å / Num. obs: 5912 / % possible obs: 95.4 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.079 / Rrim(I) all: 0.152 / Rsym value: 0.144 / Net I/av σ(I): 4.5 / Net I/σ(I): 4.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 406 / CC1/2: 0.567 / Rpim(I) all: 0.417 / Rrim(I) all: 0.842 / Rsym value: 0.656 / % possible all: 97.3

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Processing

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

1rop


Resolution: 2→34 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.706 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28747 301 5.1 %RANDOM
Rwork0.23875 ---
obs0.2411 5585 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.393 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å2-1.41 Å2
2---0.77 Å20 Å2
3----1.84 Å2
Refinement stepCycle: 1 / Resolution: 2→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 16 24 920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02913
X-RAY DIFFRACTIONr_bond_other_d0.0010.02924
X-RAY DIFFRACTIONr_angle_refined_deg1.15721214
X-RAY DIFFRACTIONr_angle_other_deg0.62532155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.215109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6825.12241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14815206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.052156
X-RAY DIFFRACTIONr_chiral_restr0.060.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02949
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_it5.3223.895430
X-RAY DIFFRACTIONr_mcbond_other5.063.874429
X-RAY DIFFRACTIONr_mcangle_it7.8495.769535
X-RAY DIFFRACTIONr_mcangle_other7.8685.787536
X-RAY DIFFRACTIONr_scbond_it8.1384.952483
X-RAY DIFFRACTIONr_scbond_other8.134.955484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.547.034678
X-RAY DIFFRACTIONr_long_range_B_refined16.08273.0313553
X-RAY DIFFRACTIONr_long_range_B_other16.0873.0383554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 24 -
Rwork0.48 378 -
obs--96.17 %

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