SAXSdb — 9yio

▼

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

PvRipr EGF7-8

Plasmodium vivax

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 764–843	Mutation：N767Q, N780Q	5B3 kappa chain × 1 5B3 heavy chain × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.4；295 K；0.2M (NH4)2SO4, 20% PEG-3,350 and 0.1M Sodium Acetate buffer pH 4.4	Resolution 2.08 Å R-free 0.235

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A564ZTL5_PLAVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 4–83； UniProt 764–843

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yio
Deposition date deposition_date	2025-10-02
Structure title title	Crystal structure of 5B3 Fab in complex with PvRipr EGF7-8
Keywords keywords	Plasmodium vivax, invasion, antibody-antigen complex, CELL INVASION; CELL INVASION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	28.45 Å
Radius of gyration Rg (electron density) rg_electron	28.16 Å
Forward intensity I(0) i0	55144200.00
Molecular weight molecular_weight	56631.0 kDa
Excluded volume excluded_volume	70229 Å³
Envelope volume envelope_volume	90335 Å³
Hydration-shell volume shell_volume	28200 Å³
Envelope diameter envelope_diameter	102.8 Å
Shell Rg shell_rg	33.69 Å
Envelope Rg envelope_rg	28.24 Å
Shape Rg shape_rg	28.07 Å
Total Rg total_rg	28.98 Å
Total atoms total_atoms	3970
Residues n_residues	506
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

▼

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

Maximum dimension Dmax dmax	97.5 Å
Rg (real space) rg_real	28.64 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	5.5140e+07
I(0) uncertainty (real space) i0_real_error	8.9980e+05
Rg (reciprocal space) rg_reciprocal	28.58 Å
I(0) (reciprocal space) i0_reciprocal	55140000.0000
Solution quality estimate total_estimate	0.8667
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.6 Å
Skewness Skewness skewness	0.497
Kurtosis Kurtosis kurtosis	-0.175
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7298000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.952

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PvRipr EGF7-8
Molecular weight formula_weight	9509.1 kDa
Mutation mutation	N767Q, N780Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4214

GHMYCKQVTCKENEICKVVQNTPTCECKENLKRDSNNECVFNNMCLVNKGNCPIDSECIYHEKKRHQCLCHKKGLVAINGKCV

来源 Source

来源生物 organism	Plasmodium vivax
通用名 common_name	malaria parasite P. vivax
NCBI Class编号 ncbi_taxonomy_id	5855
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	5B3 kappa chain
Molecular weight formula_weight	23237.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QIVLSQSPAILSASPGEKVTMTCRASSSVNYMHWYQQKPGSSPKPWIYATSNLASGVPTRFSGSGSGTSYSLTISRVEAEDAATYYCQQWSPNPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNNRGE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	5B3 heavy chain
Molecular weight formula_weight	24167.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

EVQVQQSGTELVRPGAVVKLSCIVSGFSIKDYYIHWVKQRPEKGLEWIGWIDPENGKTIYDPKFQGKASITADRSFNTAYLHISRPTSEDTAVYYCARSYYYGSSDAMDNWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

▶

8. Citations (1)

▶

Unit-cell length a length_a	80.270 Å
Unit-cell length b length_b	81.746 Å
Unit-cell length c length_c	92.149 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	48.640 Å
R factor r_factor	0.2058
R_work r_work	0.2041
R_free r_free	0.2354

fit	/app/data/saxs_computation/yi/9yio/9yio.fit
pddf	/app/data/pr_computation/yi/9yio/9yio.pr.out
profile	/app/data/saxs_computation/yi/9yio/9yio.dat

Crystal structure of 5B3 Fab in complex with PvRipr EGF7-8

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

PvRipr EGF7-8

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)