SAXSdb — 3njv

▼

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	Other combination	Monomer	Protein 1 其他Polymer 1	;alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid ; × 1 CALCIUM ION × 1 SULFATE ION × 3 water × 1	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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3njv
Deposition date deposition_date	2010-06-18
Structure title title	Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex
Keywords keywords	Carbohydrate active enzyme, Lyase, Pectin degradation, Polysaccharide Lyase Family 4; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3njv__assembly_1__model_1

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

Download this curve (.dat)

3njv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3njv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.26 Å
Rg (electron density)	24.66 Å
Total Rg	25.46 Å
Atom count	3894
Residues	508
Excluded volume	68200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3njv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Rhamnogalacturonase B
Molecular weight formula_weight	54185.4 kDa
EC 编号 ec_number	4.2.2.10
Mutation mutation	K150A
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	4264

AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSAFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGHVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ

Source Source

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

Entity 2 Entity 2 branched

Description description	;alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid ;
Molecular weight formula_weight	984.8 kDa
Source method src_method	man
Copy count entity_count	1

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	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	362

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3njva1
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

Domain ID domain_id	d3njva2
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	d3njva3
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

CATH v4.4 (3 domains)

Domain ID domain_id	3njvA01
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	3njvA02
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	3njvA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

▶

Unit-cell length a length_a	76.974 Å
Unit-cell length b length_b	76.974 Å
Unit-cell length c length_c	170.649 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	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1882
R_work r_work	0.1847
R_free r_free	0.2524

Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex

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

3njv__assembly_1__model_1

3njv__assembly_1__model_1 | I(q)

3njv__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex

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

3njv__assembly_1__model_1

3njv__assembly_1__model_1 | I(q)

3njv__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)