SAXSdb — 7s5a

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

C-C motif chemokine 8

Homo sapiens

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 24–99 Chain B； UniProt 24–99	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium phosphate dibasic 20% w/v Polyethylene glycol 3,350 pH 8	Resolution 1.37 Å R-free 0.189

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 7S5A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ESR CRYSTAL STRUCTURE OF HUMAN MONOCYTE CHEMOTACTIC PROTEIN-2 Deposited 2000-04-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–99（76 aa）	Mutation：Q24(PCA) AND K69Q Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；Ammonium sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.320
7S59 Crystal structure of the tick evasin EVA-P974 complexed to a chimera made of human chemokines CCL7 and CCL8 Deposited 2021-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain 2 24–38（15 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M TRIS 8.5 pH (Buffer) 2 M (NH4)2SO4 (Precipitant)	Resolution 2.39 Å R-free 0.268
7S59 Crystal structure of the tick evasin EVA-P974 complexed to a chimera made of human chemokines CCL7 and CCL8 Deposited 2021-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain 4 24–38（15 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M TRIS 8.5 pH (Buffer) 2 M (NH4)2SO4 (Precipitant)	Resolution 2.39 Å R-free 0.268

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCL8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 24–99 Author chain B； PDBConstruct 1–76； UniProt 24–99

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	7s5a
Deposition date deposition_date	2021-09-10
Structure title title	Crystal structure of human chemokine CCL8
Keywords keywords	CC Chemokine, CYTOKINE; CYTOKINE
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	18.73 Å
Radius of gyration Rg (electron density) rg_electron	17.95 Å
Forward intensity I(0) i0	5347700.00
Molecular weight molecular_weight	16766.0 kDa
Excluded volume excluded_volume	21020 Å³
Envelope volume envelope_volume	26897 Å³
Hydration-shell volume shell_volume	13127 Å³
Envelope diameter envelope_diameter	60.6 Å
Shell Rg shell_rg	22.97 Å
Envelope Rg envelope_rg	17.85 Å
Shape Rg shape_rg	17.99 Å
Total Rg total_rg	18.72 Å
Total atoms total_atoms	1175
Residues n_residues	149
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	60.3 Å
Rg (real space) rg_real	18.74 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	5.3480e+06
I(0) uncertainty (real space) i0_real_error	6.3820e+04
Rg (reciprocal space) rg_reciprocal	18.74 Å
I(0) (reciprocal space) i0_reciprocal	5348000.0000
Solution quality estimate total_estimate	0.8213
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.293
Kurtosis Kurtosis kurtosis	-0.565
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1282000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.000

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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	61.807 Å
Unit-cell length b length_b	64.718 Å
Unit-cell length c length_c	81.125 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	1.370 Å
Low-resolution limit resolution_low	40.560 Å
R factor r_factor	0.1704
R_work r_work	0.1694
R_free r_free	0.1893

Description description	C-C motif chemokine 8
Molecular weight formula_weight	8928.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1422

Crystal structure of human chemokine CCL8

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

C-C motif chemokine 8

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

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	215

fit	/app/data/saxs_computation/s5/7s5a/7s5a.fit
pddf	/app/data/pr_computation/s5/7s5a/7s5a.pr.out
profile	/app/data/saxs_computation/s5/7s5a/7s5a.dat