SAXSdb — 1nkg

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

Rhamnogalacturonase B

Aspergillus aculeatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 SULFATE ION × 4 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 SULFATE ION × 8 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RHGB_ASPAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–508； UniProt 20–527

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	1nkg
Deposition date deposition_date	2003-01-03
Structure title title	Rhamnogalacturonan lyase from Aspergillus aculeatus
Keywords keywords	polysaccharide lyase, carbohydrate active enzyme, pectin, LYASE; LYASE
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.

1nkg__assembly_1__model_1

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

Download this curve (.dat)

1nkg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nkg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.42 Å
Rg (electron density)	24.84 Å
Total Rg	25.62 Å
Atom count	3836
Residues	508
Excluded volume	67158 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nkg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nkg__assembly_2__model_1`	dimeric （2）	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	Rhamnogalacturonase B
Molecular weight formula_weight	54243.5 kDa
EC 编号 ec_number	4.2.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4608

AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSKFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGHVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ

Source Source

Source organism organism	Aspergillus aculeatus
NCBI taxonomy ID ncbi_taxonomy_id	5053
Host organism host_organism	Aspergillus oryzae

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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	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	723

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1nkga1
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.1 — Starch-binding domain-like
Family Family family	b.3.1.2 — Rhamnogalacturonase B, RhgB, middle domain

Domain ID domain_id	d1nkga2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.25 — Rhamnogalacturonase B, RhgB, C-terminal domain

Domain ID domain_id	d1nkga3
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.10 — Rhamnogalacturonase B, RhgB, N-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	1nkgA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1nkgA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1120 — Carboxypeptidase-like, regulatory domain

Domain ID domain_id	1nkgA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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Unit-cell length a length_a	77.009 Å
Unit-cell length b length_b	77.009 Å
Unit-cell length c length_c	170.787 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	19.910 Å
R factor r_factor	0.1640
R_work r_work	0.1640
R_free r_free	0.1860

Rhamnogalacturonan lyase from Aspergillus aculeatus

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

Rhamnogalacturonase B

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

1nkg__assembly_1__model_1

1nkg__assembly_1__model_1 | I(q)

1nkg__assembly_1__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Rhamnogalacturonan lyase from Aspergillus aculeatus

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

Rhamnogalacturonase B

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

1nkg__assembly_1__model_1

1nkg__assembly_1__model_1 | I(q)

1nkg__assembly_1__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)