SAXSdb — 3fpt

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

Evasin-1

Rhipicephalus sanguineus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–114	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；23% (w/v) PEG 4000, 300mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.70 Å R-free 0.305
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 21–114	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；23% (w/v) PEG 4000, 300mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.70 Å R-free 0.305
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 21–114	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；23% (w/v) PEG 4000, 300mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.70 Å R-free 0.305

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 3FPT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FPR Crystal Structure of Evasin-1 Deposited 2009-01-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–114（94 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；3% (w/v) PEG 4000, 200mM Ammonium Sulfate, 10% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.63 Å R-free 0.265
3FPR Crystal Structure of Evasin-1 Deposited 2009-01-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 21–114（94 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；3% (w/v) PEG 4000, 200mM Ammonium Sulfate, 10% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.63 Å R-free 0.265
3FPU The crystallographic structure of the Complex between Evasin-1 and CCL3 Deposited 2009-01-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–114（94 aa）	Not recorded	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；291 K；24% (w/v) PEG 3350, 200mM Ammonium sulfate, 100mM HEPES, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.76 Å R-free 0.285

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

View Construct and Data Evidence

UniProt name	EVA1_RHISA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 21–114 Author chain B； PDBConstruct 1–94； UniProt 21–114 Author chain C； PDBConstruct 1–94； UniProt 21–114

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	3fpt
Deposition date deposition_date	2009-01-06
Structure title title	The Crystal Structure of the Complex between Evasin-1 and CCL3
Keywords keywords	novel fold, glycosylated protein, Glycoprotein, Secreted, IMMUNE SYSTEM; IMMUNE SYSTEM
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	21.86 Å
Radius of gyration Rg (electron density) rg_electron	21.31 Å
Forward intensity I(0) i0	16770200.00
Molecular weight molecular_weight	28493.0 kDa
Excluded volume excluded_volume	34638 Å³
Envelope volume envelope_volume	43408 Å³
Hydration-shell volume shell_volume	18202 Å³
Envelope diameter envelope_diameter	82.2 Å
Shell Rg shell_rg	26.81 Å
Envelope Rg envelope_rg	21.82 Å
Shape Rg shape_rg	21.28 Å
Total Rg total_rg	22.13 Å
Total atoms total_atoms	1979
Residues n_residues	249
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	78.7 Å
Rg (real space) rg_real	22.05 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	1.6770e+07
I(0) uncertainty (real space) i0_real_error	2.4550e+05
Rg (reciprocal space) rg_reciprocal	22.01 Å
I(0) (reciprocal space) i0_reciprocal	16770000.0000
Solution quality estimate total_estimate	0.8207
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.586
Kurtosis Kurtosis kurtosis	0.007
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1953000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.737; Smooth: 0.967

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Evasin-1
Molecular weight formula_weight	11306.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2007

EDDEDYGDLGGCPFLVAENKTGYPTIVACKQDCNGTTETAPNGTRCFSIGDEGLRRMTANLPYDCPLGQCSNGDCIPKETYEVCYRRNWRDKKNHHHHHH

来源 Source

来源生物 organism	Rhipicephalus sanguineus
通用名 common_name	Brown dog tick
NCBI Class编号 ncbi_taxonomy_id	34632
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3fptA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fptB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3fptC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	100 —

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8. Citations (3)

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Unit-cell length a length_a	68.704 Å
Unit-cell length b length_b	70.491 Å
Unit-cell length c length_c	103.819 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	32.620 Å
R factor r_factor	0.2301
R_work r_work	0.2261
R_free r_free	0.3052

fit	/app/data/saxs_computation/fp/3fpt/3fpt.fit
pddf	/app/data/pr_computation/fp/3fpt/3fpt.pr.out
profile	/app/data/saxs_computation/fp/3fpt/3fpt.dat

The Crystal Structure of the Complex between Evasin-1 and CCL3

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

Evasin-1

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