SAXSdb — 4bqb

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

NEOGENIN

MUS MUSCULUS

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 883–1133	Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 883–1133	Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 883–1133	Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 883–1133	Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223

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 4BQB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BQ6 Crystal structure of the RGMB-NEO1 complex form 1 Deposited 2013-05-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5 0.2 M SODIUM ACETATE 30% PEG4000	Resolution 2.30 Å R-free 0.267
4BQ6 Crystal structure of the RGMB-NEO1 complex form 1 Deposited 2013-05-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5 0.2 M SODIUM ACETATE 30% PEG4000	Resolution 2.30 Å R-free 0.267
4BQ7 Crystal structure of the RGMB-Neo1 complex form 2 Deposited 2013-05-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5, 0.2 M LITHIUM SULPHATE, 25 % PEG3350	Resolution 6.60 Å R-free 0.280
4BQ7 Crystal structure of the RGMB-Neo1 complex form 2 Deposited 2013-05-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5, 0.2 M LITHIUM SULPHATE, 25 % PEG3350	Resolution 6.60 Å R-free 0.280
4BQ8 Crystal structure of the RGMB-NEO1 complex form 3 Deposited 2013-05-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 883–1083（201 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1083	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1 M SODIUM ACETATE, PH 4.6, 0.18 M POTASSIUM ACETATE, 18 % PEG 3350	Resolution 2.80 Å R-free 0.199
4BQ9 Crystal structure of the FN5 and FN6 domains of NEO1, form 1 Deposited 2013-05-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 883–1083（201 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1083	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5, 0.2 M SODIUM ACETATE, 30% PEG4000	Resolution 2.91 Å R-free 0.230
4BQ9 Crystal structure of the FN5 and FN6 domains of NEO1, form 1 Deposited 2013-05-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 883–1083（201 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1083	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5, 0.2 M SODIUM ACETATE, 30% PEG4000	Resolution 2.91 Å R-free 0.230
4BQC Crystal structure of the FN5 and FN6 domains of NEO1 bound to SOS Deposited 2013-05-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.15 M POTASSIUM NITRATE, 15% PEG3350, pH 8.5	Resolution 3.20 Å R-free 0.259
4BQC Crystal structure of the FN5 and FN6 domains of NEO1 bound to SOS Deposited 2013-05-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.15 M POTASSIUM NITRATE, 15% PEG3350, pH 8.5	Resolution 3.20 Å R-free 0.259
4PLN Crystal Structure of Chicken Netrin-1 (LN-LE3) complexed with mouse Neogenin (FN4-5) Deposited 2014-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 765–964（200 aa） Fragment：FN4-5 (UNP residues 765-964) Chain D 765–964（200 aa） Fragment：FN4-5 (UNP residues 765-964)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Hepes pH 7.0, 12% PEG3350	Resolution 3.20 Å R-free 0.239
4UI2 Crystal structure of the ternary RGMB-BMP2-NEO1 complex Deposited 2015-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 883–1133（251 aa） Fragment：5TH AND 6TH FN TYPE 3 LIKE DOMAINS	Not recorded	SRT S,R MESO-TARTARIC ACID × 6 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 1.5 M AMMONIUM SULPHATE, 12% (V/V) GLYCEROL	Resolution 3.15 Å R-free 0.236
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain E 883–1123（241 aa） Chain F 883–1123（241 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000	Resolution 5.50 Å R-free 0.428
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain K 883–1123（241 aa） Chain L 883–1123（241 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000	Resolution 5.50 Å R-free 0.428
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 883–1123（241 aa） Chain R 883–1123（241 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000	Resolution 5.50 Å R-free 0.428

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEO1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–254； UniProt 883–1133 Author chain B； PDBConstruct 4–254； UniProt 883–1133 Author chain C； PDBConstruct 4–254； UniProt 883–1133 Author chain D； PDBConstruct 4–254； UniProt 883–1133

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	4bqb
Deposition date deposition_date	2013-05-30
Structure title title	Crystal structure of the FN5 and FN6 domains of NEO1, form 2
Keywords keywords	CELL ADHESION; CELL ADHESION
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	31.46 Å
Radius of gyration Rg (electron density) rg_electron	30.55 Å
Forward intensity I(0) i0	125001000.00
Molecular weight molecular_weight	89901.0 kDa
Excluded volume excluded_volume	113200 Å³
Envelope volume envelope_volume	151430 Å³
Hydration-shell volume shell_volume	41694 Å³
Envelope diameter envelope_diameter	108.3 Å
Shell Rg shell_rg	37.55 Å
Envelope Rg envelope_rg	30.18 Å
Shape Rg shape_rg	30.48 Å
Total Rg total_rg	31.43 Å
Total atoms total_atoms	6337
Residues n_residues	792
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	100.6 Å
Rg (real space) rg_real	31.33 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.2500e+08
I(0) uncertainty (real space) i0_real_error	1.9080e+06
Rg (reciprocal space) rg_reciprocal	31.39 Å
I(0) (reciprocal space) i0_reciprocal	125000000.0000
Solution quality estimate total_estimate	0.8888
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.2 Å
Skewness Skewness skewness	0.241
Kurtosis Kurtosis kurtosis	-0.363
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9953000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.964

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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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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4bqbA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4bqbA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4bqbB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4bqbB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4bqbC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4bqbC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4bqbD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4bqbD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	58.897 Å
Unit-cell length b length_b	97.394 Å
Unit-cell length c length_c	91.341 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2008
R_work r_work	0.1996
R_free r_free	0.2230

Description description	NEOGENIN
Molecular weight formula_weight	29221.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6337

Crystal structure of the FN5 and FN6 domains of NEO1, form 2

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

NEOGENIN

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 non-polymer

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	HOMO SAPIENS

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	4

fit	/app/data/saxs_computation/bq/4bqb/4bqb.fit
pddf	/app/data/pr_computation/bq/4bqb/4bqb.pr.out
profile	/app/data/saxs_computation/bq/4bqb/4bqb.dat