SAXSdb — 6dvu

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apolipoprotein C-I

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–83 Chain B； UniProt 1–83	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；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.	Resolution 1.80 Å R-free 0.276

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6DVU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ALE CONFORMATION OF TWO PEPTIDES CORRESPONDING TO HUMAN APOLIPOPROTEIN C-I RESIDUES 7-24 AND 35-53 IN THE PRESENCE OF SODIUM DODECYLSULFATE BY CD AND NMR SPECTROSCOPY Deposited 1995-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–50（18 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ALF CONFORMATION OF TWO PEPTIDES CORRESPONDING TO HUMAN APOLIPOPROTEIN C-I RESIDUES 7-24 AND 35-53 IN THE PRESENCE OF SODIUM DODECYLSULFATE BY CD AND NMR SPECTROSCOPY Deposited 1995-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–79（19 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1IOJ HUMAN APOLIPOPROTEIN C-I, NMR, 18 STRUCTURES Deposited 1998-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–83（57 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；323 K NMR sample composition 5.8 mM native apoC-I, 90%H2O/10%D2O, 232 mM SDS-D25 \| 90% H2O/10% D2O NMR sample composition 5 mM selectively 15N-labeled synthetic apoC-I, 90%H2O/10%D2O, 200 mM SDS-D25 \| 90% H2O/10% D2O	Resolution not provided
1OPP PEPTIDE OF HUMAN APOLIPOPROTEIN C-I RESIDUES 1-38, NMR, 28 STRUCTURES Deposited 1997-05-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–64（38 aa） Fragment：RESIDUES 1 - 38	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；310 K NMR sample composition 5 mM apoC, 300 mM SDS-d2s \| 90% H2O/10% D2O NMR sample composition 5 mM apoC, 300 mM SDS-d2s \| 99.9% D2O NMR sample composition 5 mM apoC, 50 mM potassium chloride, 20 mM potassium phosphate \| 50% (v/v) TFE-d, 10% D2O	Resolution not provided
6DXR Structure of the Monoclinic-2 (Monocl-2) Crystal Form of Human Apolipoprotein C1 Deposited 2018-06-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–83（83 aa） Chain B 1–83（83 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；20% PEG	Resolution 2.00 Å R-free 0.287
6DZ6 Structure of the Orthorhombic (Orthrhmb) Crystal Form of Human Apolipoprotein C1 Deposited 2018-07-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–83（83 aa） Chain B 1–83（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；16% MPD - 18% MPD	Resolution 3.00 Å R-free 0.283
6NF3 Structure of the Monoclinic-3 (Monocln-3) Crystal Form of Human Apolipoprotein C1 Deposited 2018-12-18	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–83（83 aa） Chain B 1–83（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；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.	Resolution 2.33 Å R-free 0.318

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APOC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–83； UniProt 1–83 Author chain B； PDBConstruct 1–83； UniProt 1–83

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6dvu
Deposition date deposition_date	2018-06-25
Structure title title	Structure of the Monoclinic-1 (Monocl-1) Crystal Form of Human Apolipoprotein C1
Keywords keywords	lipoprotein, alpha-helix, lipoprotein particles, lipid metabolism, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.05 Å
Radius of gyration Rg (electron density) rg_electron	23.84 Å
Forward intensity I(0) i0	2767710.00
Molecular weight molecular_weight	12217.0 kDa
Excluded volume excluded_volume	15515 Å³
Envelope volume envelope_volume	21601 Å³
Hydration-shell volume shell_volume	9560 Å³
Envelope diameter envelope_diameter	92.1 Å
Shell Rg shell_rg	25.38 Å
Envelope Rg envelope_rg	24.28 Å
Shape Rg shape_rg	23.80 Å
Total Rg total_rg	24.24 Å
Total atoms total_atoms	859
Residues n_residues	104
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.4 Å
Rg (real space) rg_real	23.65 Å
Rg uncertainty (real space) rg_real_error	1.26 Å
I(0) (real space) i0_real	2.7680e+06
I(0) uncertainty (real space) i0_real_error	4.3180e+04
Rg (reciprocal space) rg_reciprocal	23.51 Å
I(0) (reciprocal space) i0_reciprocal	2767000.0000
Solution quality estimate total_estimate	0.6802
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.3 Å
Skewness Skewness skewness	0.728
Kurtosis Kurtosis kurtosis	-0.027
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	164800.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.268; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.038; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	29.541 Å
Unit-cell length b length_b	46.739 Å
Unit-cell length c length_c	33.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	33.000 Å
R factor r_factor	0.2243
R_work r_work	0.2214
R_free r_free	0.2763

Description description	Apolipoprotein C-I
Molecular weight formula_weight	9344.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	894

Structure of the Monoclinic-1 (Monocl-1) Crystal Form of Human Apolipoprotein C1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Apolipoprotein C-I

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

fit	/app/data/saxs_computation/dv/6dvu/6dvu.fit
pddf	/app/data/pr_computation/dv/6dvu/6dvu.pr.out
profile	/app/data/saxs_computation/dv/6dvu/6dvu.dat