SAXSdb — 2xn4

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

KELCH-LIKE PROTEIN 2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 294–591	Fragment：KELCH DOMAIN, RESIDUES 294-591	NA SODIUM ION × 1 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.2M (NH4)2SO4, 0.1M MES PH 6.5, 30% PEG 5000 MME, 0.2M NASCN	Resolution 1.99 Å R-free 0.222
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 294–591	Fragment：KELCH DOMAIN, RESIDUES 294-591	NA SODIUM ION × 1 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.2M (NH4)2SO4, 0.1M MES PH 6.5, 30% PEG 5000 MME, 0.2M NASCN	Resolution 1.99 Å R-free 0.222

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 2XN4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4CHB Crystal structure of the human KLHL2 Kelch domain in complex with a WNK4 peptide Deposited 2013-11-29	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 294–591（298 aa） Fragment：KELCH DOMAIN, RESIDUES 294-591	Not recorded	EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 2 12P DODECAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；SITTING-DROP VAPOUR-DIFFUSION, 2.5 M AMMONIUM SULPHATE, 0.1 M HEPES, 2 % PEG 400 (PH 7.2), 293 K	Resolution 1.56 Å R-free 0.194
4CHB Crystal structure of the human KLHL2 Kelch domain in complex with a WNK4 peptide Deposited 2013-11-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 294–591（298 aa） Fragment：KELCH DOMAIN, RESIDUES 294-591	Not recorded	EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；SITTING-DROP VAPOUR-DIFFUSION, 2.5 M AMMONIUM SULPHATE, 0.1 M HEPES, 2 % PEG 400 (PH 7.2), 293 K	Resolution 1.56 Å R-free 0.194

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

View Construct and Data Evidence

UniProt name	KLHL2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–300； UniProt 294–591 Author chain B； PDBConstruct 3–300； UniProt 294–591

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	2xn4
Deposition date deposition_date	2010-07-30
Structure title title	Crystal structure of the kelch domain of human KLHL2 (Mayven)
Keywords keywords	STRUCTURAL PROTEIN, CYTOSKELETON; STRUCTURAL 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	25.49 Å
Radius of gyration Rg (electron density) rg_electron	25.14 Å
Forward intensity I(0) i0	70992600.00
Molecular weight molecular_weight	62250.0 kDa
Excluded volume excluded_volume	76456 Å³
Envelope volume envelope_volume	89828 Å³
Hydration-shell volume shell_volume	29730 Å³
Envelope diameter envelope_diameter	83.9 Å
Shell Rg shell_rg	32.64 Å
Envelope Rg envelope_rg	25.26 Å
Shape Rg shape_rg	25.18 Å
Total Rg total_rg	25.82 Å
Total atoms total_atoms	4350
Residues n_residues	572
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	79.7 Å
Rg (real space) rg_real	25.45 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	7.0990e+07
I(0) uncertainty (real space) i0_real_error	9.2490e+05
Rg (reciprocal space) rg_reciprocal	25.46 Å
I(0) (reciprocal space) i0_reciprocal	70990000.0000
Solution quality estimate total_estimate	0.7430
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.6 Å
Skewness Skewness skewness	0.319
Kurtosis Kurtosis kurtosis	-0.411
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16010000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 1.000; Smooth: 0.959

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	KELCH-LIKE PROTEIN 2
Molecular weight formula_weight	32830.3 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	4897

SMSVRTRLRTPMNLPKLMVVVGGQAPKAIRSVECYDFKEERWHQVAELPSRRCRAGMVYMAGLVFAVGGFNGSLRVRTVDSYDPVKDQWTSVANMRDRRSTLGAAVLNGLLYAVGGFDGSTGLSSVEAYNIKSNEWFHVAPMNTRRSSVGVGVVGGLLYAVGGYDVASRQCLSTVECYNATTNEWTYIAEMSTRRSGAGVGVLNNLLYAVGGHDGPLVRKSVEVYDPTTNAWRQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPTTDKWTVVSSCMSTGRSYAGVTVIDKRL

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	537

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2xn4a_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.11 — Kelch motif
Family Family family	b.68.11.0 — automated matches

Domain ID domain_id	d2xn4b_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.11 — Kelch motif
Family Family family	b.68.11.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2xn4A00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	80 — Kelch-type beta propeller

Domain ID domain_id	2xn4B00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	80 — Kelch-type beta propeller

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8. Citations (1)

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Unit-cell length a length_a	45.994 Å
Unit-cell length b length_b	46.005 Å
Unit-cell length c length_c	71.762 Å
Unit-cell angle α angle_alpha	86.68 °
Unit-cell angle β angle_beta	82.75 °
Unit-cell angle γ angle_gamma	68.48 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	19.820 Å
R factor r_factor	0.1719
R_work r_work	0.1693
R_free r_free	0.2215

fit	/app/data/saxs_computation/xn/2xn4/2xn4.fit
pddf	/app/data/pr_computation/xn/2xn4/2xn4.pr.out
profile	/app/data/saxs_computation/xn/2xn4/2xn4.dat

Crystal structure of the kelch domain of human KLHL2 (Mayven)

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

KELCH-LIKE PROTEIN 2

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