SAXSdb — 2rbl

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

Tenascin

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 802–893 Chain B； UniProt 802–893	Fragment：unp residues 802-896 Mutation：M24F, P25K, S27L, Q28A, P29E, V30I, F33I	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3；298 K；2.0 M Ammonium Sulfate, pH = 3.0, 10% additive 0.1 M cupric chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.300
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain M； UniProt 802–893	Fragment：unp residues 802-896 Mutation：M24F, P25K, S27L, Q28A, P29E, V30I, F33I	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3；298 K；2.0 M Ammonium Sulfate, pH = 3.0, 10% additive 0.1 M cupric chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.300

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 2RBL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TEN STRUCTURE OF A FIBRONECTIN TYPE III DOMAIN FROM TENASCIN PHASED BY MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN Deposited 1992-08-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 802–891（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
2RB8 High resolution design of a protein loop Deposited 2007-09-18	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 802–893（92 aa） Fragment：unp residues 802-896	Mutation：M24F, P25K, S27L, Q28A, P29E, V30I, F33I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；3.8M sodium formate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.45 Å R-free 0.196
6QNV Fibrinogen-like globe domain of Human Tenascin-C Deposited 2019-02-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1979–2196（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Morpheus 0.09M NPS, 0.1M Buffer System 3 pH = 8.5, 50% v/v Precipitant Mix 1	Resolution 1.40 Å R-free 0.182
8FN8 Crystal structure of the C-terminal Fg domain of TNC with the single FN domain of PTPRZ Deposited 2022-12-27	Different construct Different mutation/modification 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 1975–2201（227 aa） Fragment：Fg domain (UNP residues 1975-2201)	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% w/v PEG3350, 100 mM Tris-HCl, pH 8.0	Resolution 1.89 Å R-free 0.205
8FNB Crystal structure of the C-terminal Fg domain of human TNC with the mutations Y2140H and S2164H Deposited 2022-12-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1975–2201（227 aa） Fragment：Fg domain (UNP residues 1975-2201)	Mutation：Y2140H, S2164H	CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；200 mM lithium sulfate, 25% PEG1500, 50 mM Tris, pH 8.0	Resolution 1.80 Å R-free 0.174
8FNB Crystal structure of the C-terminal Fg domain of human TNC with the mutations Y2140H and S2164H Deposited 2022-12-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1975–2201（227 aa） Fragment：Fg domain (UNP residues 1975-2201)	Mutation：Y2140H, S2164H	CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；200 mM lithium sulfate, 25% PEG1500, 50 mM Tris, pH 8.0	Resolution 1.80 Å R-free 0.174
9NIG PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 1013–1024（12 aa） Fragment：residues 1013-1024	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350	Resolution 3.20 Å R-free 0.260
9NIG PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 1013–1024（12 aa） Fragment：residues 1013-1024	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350	Resolution 3.20 Å R-free 0.260
9NIG PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 1013–1024（12 aa） Fragment：residues 1013-1024	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH7.5, 0.3M NaCl, 0.05 M Glutamic acid, 0.05M Arginine, 20% PEG3350	Resolution 3.20 Å R-free 0.260
9NIH Crystal structure of HLA-DR4 presenting citrullinated Tenascin C peptide Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1013–1024（12 aa） Fragment：residues 1013-1024	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.2 M NaCl, 0.1 M Bis Tris pH 5.5, 29% PEG3350	Resolution 2.40 Å R-free 0.219
9R5Y Crystal structure of the C-terminal domain of human TNC in complex with Adhiron 52 Deposited 2025-05-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1976–2193（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291.15 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.40 Å R-free 0.185
9R5Y Crystal structure of the C-terminal domain of human TNC in complex with Adhiron 52 Deposited 2025-05-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1976–2193（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291.15 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.40 Å R-free 0.185

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TENA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–93； UniProt 802–893 Author chain B； PDBConstruct 2–93； UniProt 802–893 Author chain M； PDBConstruct 2–93； UniProt 802–893

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	2rbl
Deposition date deposition_date	2007-09-19
Structure title title	High resolution design of a protein loop
Keywords keywords	;Beta sheet, loop design, Alternative splicing, Cell adhesion, Coiled coil, EGF-like domain, Extracellular matrix, Glycoprotein, Phosphorylation, Polymorphism, Secreted ;; 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	23.03 Å
Radius of gyration Rg (electron density) rg_electron	22.71 Å
Forward intensity I(0) i0	15163800.00
Molecular weight molecular_weight	28598.0 kDa
Excluded volume excluded_volume	35422 Å³
Envelope volume envelope_volume	44904 Å³
Hydration-shell volume shell_volume	17856 Å³
Envelope diameter envelope_diameter	76.9 Å
Shell Rg shell_rg	27.73 Å
Envelope Rg envelope_rg	22.72 Å
Shape Rg shape_rg	22.72 Å
Total Rg total_rg	23.35 Å
Total atoms total_atoms	2009
Residues n_residues	258
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	75.8 Å
Rg (real space) rg_real	23.15 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.5160e+07
I(0) uncertainty (real space) i0_real_error	1.9270e+05
Rg (reciprocal space) rg_reciprocal	23.12 Å
I(0) (reciprocal space) i0_reciprocal	15160000.0000
Solution quality estimate total_estimate	0.6919
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.433
Kurtosis Kurtosis kurtosis	-0.425
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3930000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 0.171; Positv: 1.000; Valcen: 0.864; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2rbla_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d2rblb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d2rblm_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

CATH v4.4 (4 domains)

Domain ID domain_id	2rblA01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2rblA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2rblB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2rblM00
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	137.200 Å
Unit-cell length b length_b	137.200 Å
Unit-cell length c length_c	86.682 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	54

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2500
R_work r_work	0.2500
R_free r_free	0.3000

Description description	Tenascin
Molecular weight formula_weight	11648.8 kDa
Mutation mutation	M24F, P25K, S27L, Q28A, P29E, V30I, F33I
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,M
Atom count atom_count	2009

High resolution design of a protein loop

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

Tenascin

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/rb/2rbl/2rbl.fit
pddf	/app/data/pr_computation/rb/2rbl/2rbl.pr.out
profile	/app/data/saxs_computation/rb/2rbl/2rbl.dat