SAXSdb — 2y8n

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

4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT

CLOSTRIDIUM SCATOLOGENES

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT × 2 （Q38HX3） IRON/SULFUR CLUSTER × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT × 1 （Q38HX3） IRON/SULFUR CLUSTER × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT × 1 （Q38HX3） IRON/SULFUR CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HPDL_CLOSL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–897； UniProt 1–897 Author chain C； PDBConstruct 1–897； UniProt 1–897

4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT

CLOSTRIDIUM SCATOLOGENES

UniProt Q38HX3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT × 2 （Q38HX4） IRON/SULFUR CLUSTER × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT × 1 （Q38HX4） IRON/SULFUR CLUSTER × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT × 1 （Q38HX4） IRON/SULFUR CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HPDS_CLOSL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–86； UniProt 1–86 Author chain D； PDBConstruct 1–86； UniProt 1–86

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	2y8n
Deposition date deposition_date	2011-02-08
Structure title title	Crystal structure of glycyl radical enzyme
Keywords keywords	LYASE, RADICAL CHEMISTRY, METALLOENZYME, IRON-SULFUR CENTER; 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.

2y8n__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2y8n__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y8n__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.26 Å
Rg (electron density)	27.21 Å
Total Rg	28.12 Å
Atom count	7496
Residues	955
Excluded volume	133480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y8n__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2y8n__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2y8n__assembly_3__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	4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
Molecular weight formula_weight	100745.5 kDa
EC 编号 ec_number	4.1.1.83
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17094

MNVKETKLEDVLKSRGIDMKDAYNISEADIPEAKESTQKLMDIYYTLKVTADMEAAYWYNRTWWENDGEVIEVRRAKAVAASLSHMTPTILPYEKLVMNKTKNVRGAFPFPWVCASFFNAQAEALMNEVDAPAENEADSVSVVGAGGGNVTESYGNVISIAKKFGMRKEEIPVLVKTSKPWEGISVEELSNKYSKMTPGYDQFKNIMESVICMFDSFAIPQGREVINYYMPLQYGFDGIIKLCDEKIAEVMGEAGDDGDFGMSRGYYYAAMKEITKGLSAWCENYSKRAKYLASIETDSEIKANYEKIEEVMGNIAHKKPANFWEAIQMTLCCHFGVVNEDPQSGLSIGRLGQVLQPFYEKDVEDGIMTDEEVIELLELYRIKITCIECFASAGVSGGVLSGNTFNNLSLGGQNYDGLSAVTPLEYLIVEAGMRNQTPQPTLSVLYDEKTPEDFLMKAASCTKLGLGYPAWMNNQTGMNFMMRNYGPEGMDLHDARAWCLGGCLESAPGCFLPLEYNGKVTMIPGGASPTCGTGVHFIGMPKVLELVLTNGLDKRTGKQVYPPHNKKLDSYETMVNQWKEYMELTTDVVNRCNNIQMDIWRKYNMPAVNSLLKPDCFKKGKHIGTMGARYNSCINFESCGTITFVNSLSSIKKNVFDDSKFTIEEMTDAMLNNFGFKTAYETEVFSPDFRESTDKSTKYEKIFAACVNAPKYGNADKYADEIFKAYHYYIYDMTHKFRSYYGKPLYLCQISVSTHGPQGFVTLATADGRLAGTTYSDGSVSAAAGTDKNGIYAIFESATVYDHSMHQNAQMNLKLHPTAVKGINGTRKLLDLVRAYMRKGGFHVQFNVVDSKTLRDAQLTPEKYRELMVRVAGFTQYWCEIGKPIQDEVIYRTEYDK

Source Source

Source organism organism	CLOSTRIDIUM SCATOLOGENES
NCBI taxonomy ID ncbi_taxonomy_id	1548
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT
Molecular weight formula_weight	9353.6 kDa
EC 编号 ec_number	4.1.1.83
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MRHYDCKNYINLDCEKGLCALTKGMVPIDGEGSEACPNFKPAEKCGNCKNFCNPDKYGLGTCTGLEKENWAYATCGASACPSYKAE

Source Source

Source organism organism	CLOSTRIDIUM SCATOLOGENES
NCBI taxonomy ID ncbi_taxonomy_id	1548
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 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	2114

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2y8nA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2y8nB01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2y8nB02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2y8nC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2y8nD01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2y8nD02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	132.280 Å
Unit-cell length b length_b	227.760 Å
Unit-cell length c length_c	148.010 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	29.184 Å
R factor r_factor	0.1865
R_work r_work	0.1843
R_free r_free	0.2278

Crystal structure of glycyl radical enzyme

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

4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT

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

2y8n__assembly_3__model_1

2y8n__assembly_3__model_1 | I(q)

2y8n__assembly_3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of glycyl radical enzyme

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

4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT

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

2y8n__assembly_3__model_1

2y8n__assembly_3__model_1 | I(q)

2y8n__assembly_3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)