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- PDB-6dz6: Structure of the Orthorhombic (Orthrhmb) Crystal Form of Human Ap... -

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Basic information

Entry
Database: PDB / ID: 6dz6
TitleStructure of the Orthorhombic (Orthrhmb) 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 / lipase inhibitor activity / VLDL assembly / negative regulation of cholesterol transport / phospholipase inhibitor activity / negative regulation of lipoprotein lipase activity / VLDL clearance / negative regulation of very-low-density lipoprotein particle clearance / plasma lipoprotein particle remodeling / very-low-density lipoprotein particle assembly ...negative regulation of phosphatidylcholine catabolic process / lipase inhibitor activity / VLDL assembly / negative regulation of cholesterol transport / phospholipase inhibitor activity / negative regulation of lipoprotein lipase activity / VLDL clearance / negative regulation of very-low-density lipoprotein particle clearance / plasma lipoprotein particle remodeling / very-low-density lipoprotein particle assembly / regulation of cholesterol transport / negative regulation of lipid metabolic process / lipoprotein 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 / chylomicron / high-density lipoprotein particle remodeling / phosphatidylcholine binding / phospholipid efflux / very-low-density lipoprotein particle / high-density lipoprotein particle / triglyceride metabolic process / cholesterol efflux / 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: 3 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
DepositionJul 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 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 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-11 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.459, 53.698, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 14 / 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: 1.76 Å3/Da / Density % sol: 30.2 % / Description: rectangular blocks
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 16% MPD - 18% MPD / PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Aug 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: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 29.469 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2827 122 4.6 %RANDOM
Rwork0.22389 ---
obs0.22702 2538 92.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.741 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2--2.12 Å20 Å2
3----6.09 Å2
Refinement stepCycle: 1 / Resolution: 3→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 0 14 857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019861
X-RAY DIFFRACTIONr_bond_other_d0.0010.02861
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9841140
X-RAY DIFFRACTIONr_angle_other_deg0.79132012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8755102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9892540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.09115200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.724156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02168
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_it5.5385.98411
X-RAY DIFFRACTIONr_mcbond_other5.5395.969410
X-RAY DIFFRACTIONr_mcangle_it8.5388.952512
X-RAY DIFFRACTIONr_mcangle_other8.5328.964513
X-RAY DIFFRACTIONr_scbond_it9.1257.58450
X-RAY DIFFRACTIONr_scbond_other9.1157.589451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.13710.782629
X-RAY DIFFRACTIONr_long_range_B_refined18.15714.3653265
X-RAY DIFFRACTIONr_long_range_B_other18.12613.2343263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2890 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.005→3.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 4 -
Rwork0.345 86 -
obs--44.12 %

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