1nhc

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger

Method: X-RAY DIFFRACTION

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

Polygalacturonase I

Aspergillus niger

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	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-mannopyranose × 2 SULFATE ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose × 2 SULFATE ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	alpha-D-mannopyranose × 2 SULFATE ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-mannopyranose × 2 SULFATE ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	alpha-D-mannopyranose × 2 SULFATE ION × 4 GLYCEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	alpha-D-mannopyranose × 1 SULFATE ION × 2 GLYCEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGL1_ASPNG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–336； UniProt 33–368 Author chain B； PDBConstruct 1–336； UniProt 33–368 Author chain C； PDBConstruct 1–336； UniProt 33–368 Author chain D； PDBConstruct 1–336； UniProt 33–368 Author chain E； PDBConstruct 1–336； UniProt 33–368 Author chain F； PDBConstruct 1–336； UniProt 33–368

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	1nhc
Deposition date deposition_date	2002-12-19
Structure title title	Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger
Keywords keywords	beta-helix, HYDROLASE; HYDROLASE
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.

1nhc__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1nhc__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nhc__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	21.15 Å
Rg (electron density)	20.13 Å
Total Rg	20.98 Å
Atom count	2506
Residues	336
Excluded volume	43463 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nhc__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nhc__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1nhc__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1nhc__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1nhc__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1nhc__assembly_6__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 (9)

Entity 1 Entity 1 polymer

Description description	Polygalacturonase I
Molecular weight formula_weight	34891.5 kDa
EC 编号 ec_number	3.2.1.15
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16429

STCTFTSASEASESISSCSDVVLSSIEVPAGETLDLSDAADGSTITFEGTTSFGYKEWKGPLIRFGGKDLTVTMADGAVIDGDGSRWWDSKGTNGGKTKPKFMYIHDVEDSTFKGINIKNTPVQAISVQATNVHLNDFTIDNSDGDDNGGHNTDGFDISESTGVYISGATVKNQDDCIAINSGESISFTGGTCSGGHGLSIGSVGGRDDNTVKNVTISDSTVSNSANGVRIKTIYKETGDVSEITYSNIQLSGITDYGIVIEQDYENGSPTGTPSTGIPITDVTVDGVTGTLEDDATQVYILCGDGSCSDWTWSGVDLSGGKTSDKCENVPSGASC

Source Source

Source organism organism	Aspergillus niger
NCBI taxonomy ID ncbi_taxonomy_id	5061
Host organism host_organism	Aspergillus niger

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	1

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	11

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1353

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1nhca_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

Domain ID domain_id	d1nhcb_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

Domain ID domain_id	d1nhcc_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

Domain ID domain_id	d1nhcd_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

Domain ID domain_id	d1nhce_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

Domain ID domain_id	d1nhcf_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

CATH v4.4 (6 domains)

Domain ID domain_id	1nhcA00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

Domain ID domain_id	1nhcB00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

Domain ID domain_id	1nhcC00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

Domain ID domain_id	1nhcD00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

Domain ID domain_id	1nhcE00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

Domain ID domain_id	1nhcF00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

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Unit-cell length a length_a	68.012 Å
Unit-cell length b length_b	84.130 Å
Unit-cell length c length_c	96.035 Å
Unit-cell angle α angle_alpha	114.32 °
Unit-cell angle β angle_beta	98.00 °
Unit-cell angle γ angle_gamma	89.75 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	35.810 Å
R factor r_factor	0.1760
R_work r_work	0.1750
R_free r_free	0.2090

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger

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

Polygalacturonase I

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

1nhc__assembly_5__model_1

1nhc__assembly_5__model_1 | I(q)

1nhc__assembly_5__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger

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

Polygalacturonase I

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

1nhc__assembly_5__model_1

1nhc__assembly_5__model_1 | I(q)

1nhc__assembly_5__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)