SAXSdb — 1nub

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

BASEMENT MEMBRANE PROTEIN BM-40

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	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 71–303	Fragment：FS-EC DOMAIN PAIR, FS, FOLLISTATIN-LIKE, EC, EXTRACELLULAR CALCIUM-BINDING Mutation：DEL(1-52, 196-203)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION AT ROOM TEMPERATURE. PROTEIN SOLUTION: 8-10 MG/ML IN 10 MM TRIS PH 7.5, 2 MM CACL2. RESERVOIR SOLUTION: 0.1 M HEPES PH 7.5, 12-14% (W/V) PEG4000, 10% (V/V) 2-PROPANOL., vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.306
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 71–303	Fragment：FS-EC DOMAIN PAIR, FS, FOLLISTATIN-LIKE, EC, EXTRACELLULAR CALCIUM-BINDING Mutation：DEL(1-52, 196-203)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION AT ROOM TEMPERATURE. PROTEIN SOLUTION: 8-10 MG/ML IN 10 MM TRIS PH 7.5, 2 MM CACL2. RESERVOIR SOLUTION: 0.1 M HEPES PH 7.5, 12-14% (W/V) PEG4000, 10% (V/V) 2-PROPANOL., vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.306

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 1NUB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BMO BM-40, FS/EC DOMAIN PAIR Deposited 1997-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 71–303（233 aa） Fragment：FS/EC DOMAIN PAIR, RESIDUES 53 - 286 Chain B 71–303（233 aa） Fragment：FS/EC DOMAIN PAIR, RESIDUES 53 - 286	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION AT 20 DEG C: 10 MG/ML PROTEIN IN 10 MM TRIS PH 7.5 + 2 MM CACL2; 0.1 M HEPES PH 7.5, 0.15 M NA-ACETATE, 15% PEG4K, vapor diffusion - hanging drop	Resolution 3.10 Å R-free 0.322
1SRA STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(SLASH)SPARC(SLASH)OSTEONECTIN Deposited 1995-08-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 153–303（151 aa） Fragment：CARBOXY-TERMINAL DOMAIN (RESIDUES 136 - 286)	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.249
2V53 Crystal structure of a SPARC-collagen complex Deposited 2008-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 70–212（143 aa） Fragment：FS AND EC DOMAINS, RESIDUES 70-212,221-303 Chain A 221–303（83 aa） Fragment：FS AND EC DOMAINS, RESIDUES 70-212,221-303	Not recorded	CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 3.20 Å R-free 0.320

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

View Construct and Data Evidence

UniProt name	SPRC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–229； UniProt 71–303 Author chain B； PDBConstruct 5–229； UniProt 71–303

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	1nub
Deposition date deposition_date	1997-12-05
Structure title title	HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR
Keywords keywords	EXTRACELLULAR MODULE, GLYCOPROTEIN, ANTI-ADHESIVE PROTEIN, COLLAGEN BINDING, SITE-DIRECTED MUTAGENESIS, GLYCOSYLATED PROTEIN; EXTRACELLULAR MODULE
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	32.36 Å
Radius of gyration Rg (electron density) rg_electron	32.98 Å
Forward intensity I(0) i0	48380100.00
Molecular weight molecular_weight	53435.0 kDa
Excluded volume excluded_volume	66232 Å³
Envelope volume envelope_volume	89780 Å³
Hydration-shell volume shell_volume	25646 Å³
Envelope diameter envelope_diameter	131.6 Å
Shell Rg shell_rg	35.03 Å
Envelope Rg envelope_rg	33.08 Å
Shape Rg shape_rg	33.02 Å
Total Rg total_rg	33.03 Å
Total atoms total_atoms	3732
Residues n_residues	452
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	125.9 Å
Rg (real space) rg_real	32.98 Å
Rg uncertainty (real space) rg_real_error	1.39 Å
I(0) (real space) i0_real	4.8380e+07
I(0) uncertainty (real space) i0_real_error	8.0710e+05
Rg (reciprocal space) rg_reciprocal	32.72 Å
I(0) (reciprocal space) i0_reciprocal	48370000.0000
Solution quality estimate total_estimate	0.5593
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.672
Kurtosis Kurtosis kurtosis	-0.117
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4230000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.422; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.284; Smooth: 0.989

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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	BASEMENT MEMBRANE PROTEIN BM-40
Molecular weight formula_weight	26519.3 kDa
Mutation mutation	DEL(1-52, 196-203)
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	3732

APLAPCQNHHCKHGKVCELDENNTPMCVCQDPTSCPAPIGEFEKVCSNDNKTFDSSCHFFATKCTLEGTKKGHKLHLDYIGPCKYIPPCLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLLTEKQKLRVKKIHENEKRLEAGDHPEKNYNMYIFPVHWQFGQLDQHPIDGYLSHTELAPLRAPLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDIDKDLVI

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	Homo sapiens

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1nuba1
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.3 — Osteonectin

Domain ID domain_id	d1nuba2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.3 — Follistatin (FS) module N-terminal domain, FS-N

Domain ID domain_id	d1nuba3
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.1 — Ovomucoid domain III-like

Domain ID domain_id	d1nubb1
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.3 — Osteonectin

Domain ID domain_id	d1nubb2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.3 — Follistatin (FS) module N-terminal domain, FS-N

Domain ID domain_id	d1nubb3
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.1 — Ovomucoid domain III-like

CATH v4.4 (4 domains)

Domain ID domain_id	1nubA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1nubA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1nubB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1nubB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (3)

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Unit-cell length a length_a	51.860 Å
Unit-cell length b length_b	88.140 Å
Unit-cell length c length_c	153.730 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	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2550
R_work r_work	0.2550
R_free r_free	0.3060

fit	/app/data/saxs_computation/nu/1nub/1nub.fit
pddf	/app/data/pr_computation/nu/1nub/1nub.pr.out
profile	/app/data/saxs_computation/nu/1nub/1nub.dat

HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR

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

BASEMENT MEMBRANE PROTEIN BM-40

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