SAXSdb — 1rj4

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

invertase inhibitor

Nicotiana tabacum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CADMIUM ION × 2 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CADMIUM ION × 2 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CADMIUM ION × 2 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CADMIUM ION × 2 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O49908_TOBAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–151； UniProt 20–166 Author chain B； PDBConstruct 5–151； UniProt 20–166 Author chain C； PDBConstruct 5–151； UniProt 20–166 Author chain D； PDBConstruct 5–151； UniProt 20–166

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	1rj4
Deposition date deposition_date	2003-11-18
Structure title title	Structure of a Cell Wall Invertase Inhibitor from Tobacco in Complex with Cd2+
Keywords keywords	FOUR-HELIX BUNDLE, HELICAL HAIRPIN, CADMIUM COORDINATION, BIS-TRIS BUFFER, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1rj4__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1rj4__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rj4__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.68 Å
Rg (electron density)	16.04 Å
Total Rg	16.94 Å
Atom count	1112
Residues	146
Excluded volume	20041 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rj4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rj4__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1rj4__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1rj4__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	invertase inhibitor
Molecular weight formula_weight	16088.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4692

GAMGNNLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL

Source Source

Source organism organism	Nicotiana tabacum
Common name common_name	common tobacco
NCBI taxonomy ID ncbi_taxonomy_id	4097
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	236

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rj4a_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.6 — Plant invertase/pectin methylesterase inhibitor
Family Family family	a.29.6.1 — Plant invertase/pectin methylesterase inhibitor

Domain ID domain_id	d1rj4b_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.6 — Plant invertase/pectin methylesterase inhibitor
Family Family family	a.29.6.1 — Plant invertase/pectin methylesterase inhibitor

Domain ID domain_id	d1rj4c_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.6 — Plant invertase/pectin methylesterase inhibitor
Family Family family	a.29.6.1 — Plant invertase/pectin methylesterase inhibitor

Domain ID domain_id	d1rj4d_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.6 — Plant invertase/pectin methylesterase inhibitor
Family Family family	a.29.6.1 — Plant invertase/pectin methylesterase inhibitor

CATH v4.4 (4 domains)

Domain ID domain_id	1rj4A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	40 — Invertase/pectin methylesterase inhibitor family protein

Domain ID domain_id	1rj4B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	40 — Invertase/pectin methylesterase inhibitor family protein

Domain ID domain_id	1rj4C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	40 — Invertase/pectin methylesterase inhibitor family protein

Domain ID domain_id	1rj4D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	40 — Invertase/pectin methylesterase inhibitor family protein

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Unit-cell length a length_a	59.170 Å
Unit-cell length b length_b	95.639 Å
Unit-cell length c length_c	126.191 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.670 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2550

Structure of a Cell Wall Invertase Inhibitor from Tobacco in Complex with Cd2+

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

invertase inhibitor

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1rj4__assembly_4__model_1

1rj4__assembly_4__model_1 | I(q)

1rj4__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of a Cell Wall Invertase Inhibitor from Tobacco in Complex with Cd2+

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

invertase inhibitor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1rj4__assembly_4__model_1

1rj4__assembly_4__model_1 | I(q)

1rj4__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)