SAXSdb — 9ybi

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

Metal transporter

Danio rerio

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 375–527 Chain B； UniProt 375–527	Not recorded	BEN BENZAMIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；1.1 M ammonium tartrate pH 6.5, 2% (w/v) benzamidine hydrochloride	Resolution 3.00 Å R-free 0.253

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	A2ATX7_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–158； UniProt 375–527 Author chain B； PDBConstruct 6–158； UniProt 375–527

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	9ybi
Deposition date deposition_date	2025-09-17
最后修订 last_revision	2025-09-24
Structure title title	Structure of the CBS pair domain from zebrafish magnesium transporter CNNM2
Keywords keywords	magnesium transporter, Bateman fold, adenosyl-binding domain, protein-binding domain, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	22.20 Å
Radius of gyration Rg (electron density) rg_electron	21.01 Å
Forward intensity I(0) i0	16717300.00
Molecular weight molecular_weight	31895.0 kDa
Excluded volume excluded_volume	40272 Å³
Envelope volume envelope_volume	49870 Å³
Hydration-shell volume shell_volume	19960 Å³
Envelope diameter envelope_diameter	79.9 Å
Shell Rg shell_rg	27.37 Å
Envelope Rg envelope_rg	20.97 Å
Shape Rg shape_rg	21.01 Å
Total Rg total_rg	21.90 Å
Total atoms total_atoms	2243
Residues n_residues	296
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	77.2 Å
Rg (real space) rg_real	22.14 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	1.6720e+07
I(0) uncertainty (real space) i0_real_error	2.3210e+05
Rg (reciprocal space) rg_reciprocal	22.15 Å
I(0) (reciprocal space) i0_reciprocal	16720000.0000
Solution quality estimate total_estimate	0.8690
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.194
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5505000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.995

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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	Metal transporter
Molecular weight formula_weight	17846.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2251

GPLGSLNIIQGALELRTKTVEDVMTPLRDCFMISGDAILDFATMSEIMESGYTRIPVYEGERCHIVDLLFVKDLAFVDPDDCTPLKTITKFYSHPLHFVFNDTKLDAMLEEFKKGKSHLAIVQRVNNEGEGDPFYEVLGIVTLEDVIEEIIKSEILDE

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	Zebrafish, Brachydanio rerio
NCBI Class编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	86.907 Å
Unit-cell length b length_b	147.942 Å
Unit-cell length c length_c	151.897 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	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	orthorhombic

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	46.900 Å
R factor r_factor	0.2360
R_work r_work	0.2351
R_free r_free	0.2526

fit	/app/data/saxs_computation/yb/9ybi/9ybi.fit
pddf	/app/data/pr_computation/yb/9ybi/9ybi.pr.out
profile	/app/data/saxs_computation/yb/9ybi/9ybi.dat

Structure of the CBS pair domain from zebrafish magnesium transporter CNNM2

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

Metal transporter

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