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- PDB-6nf3: Structure of the Monoclinic-3 (Monocln-3) Crystal Form of Human A... -

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Basic information

Entry
Database: PDB / ID: 6nf3
TitleStructure of the Monoclinic-3 (Monocln-3) Crystal Form of Human Apolipoprotein C1
ComponentsApolipoprotein C-I
KeywordsLIPID BINDING PROTEIN / lipoprotein particles / cholesterol / blood / vascular
Function / homology
Function and homology information


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
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: 2.33 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
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
Water1,946108
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 area1360 Å2
ΔGint-16 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.169, 49.965, 35.423
Angle α, β, γ (deg.)90.00, 105.10, 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.: 108 / 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: 1.74 Å3/Da / Density % sol: 29.51 % / Description: thin laths
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: The crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 16% to 18% 2-methyl-2,4-pentanediol (MPD) containing o.1 M sodium acetate and 0.25% ...Details: The crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 16% to 18% 2-methyl-2,4-pentanediol (MPD) containing o.1 M sodium acetate and 0.25% octyl-beta-s-1-thioglucopyanoside. The drops were equal volumes, generally 6 ul each, of the reservoir and an 8 mg/ml solution of protein dissolved in .02 M ammonium bicarbonate.
PH range: 6.0 7.0

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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: Jul 15, 1992
RadiationMonochromator: Supper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.689
11L, -K, H20.311
ReflectionResolution: 2.2→30 Å / Num. obs: 5846 / % possible obs: 70 % / Redundancy: 2.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.071 / Rrim(I) all: 0.15 / Rsym value: 0.131 / Net I/av σ(I): 4.6 / Net I/σ(I): 4.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 263 / CC1/2: 0.933 / Rpim(I) all: 0.206 / Rrim(I) all: 0.295 / Rsym value: 0.211 / % possible all: 46.2

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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: 2.33→18.97 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.618 / SU B: 13.65 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31839 226 5.2 %RANDOM
Rwork0.19879 ---
obs0.20485 4148 78.37 %-
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: 21.243 Å2
Baniso -1Baniso -2Baniso -3
1-7.82 Å20 Å2-10.95 Å2
2--9.24 Å20 Å2
3----17.06 Å2
Refinement stepCycle: 1 / Resolution: 2.33→18.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 0 108 917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019848
X-RAY DIFFRACTIONr_bond_other_d0.0010.02871
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9891126
X-RAY DIFFRACTIONr_angle_other_deg0.64332032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9245103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2072440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84215203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.832158
X-RAY DIFFRACTIONr_chiral_restr0.0530.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02173
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_it1.381.993394
X-RAY DIFFRACTIONr_mcbond_other1.3751.986393
X-RAY DIFFRACTIONr_mcangle_it2.2462.961491
X-RAY DIFFRACTIONr_mcangle_other2.2462.97492
X-RAY DIFFRACTIONr_scbond_it1.332.175454
X-RAY DIFFRACTIONr_scbond_other1.3292.182455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2293.198632
X-RAY DIFFRACTIONr_long_range_B_refined5.49135.6513203
X-RAY DIFFRACTIONr_long_range_B_other5.33235.6823162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.328→2.387 Å / Total num. of bins used: 20

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