SAXSdb — 1gnl

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

HYBRID CLUSTER PROTEIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 1 IRON/SULFUR/OXYGEN HYBRID CLUSTER × 1 ACETATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 1 IRON/SULFUR/OXYGEN HYBRID CLUSTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIS_DESDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–544； UniProt 1–544 Author chain B； PDBConstruct 1–544； UniProt 1–544

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	1gnl
Deposition date deposition_date	2001-10-05
Structure title title	Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A
Keywords keywords	HYBRID CLUSTER PROTEIN, ANAEROBIC DESULFOVIBRIO DESULFURICANS, IRON ANOMALOUS; HYBRID CLUSTER PROTEIN
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.

1gnl__assembly_1__model_1

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

Download this curve (.dat)

1gnl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1gnl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.40 Å
Rg (electron density)	22.46 Å
Total Rg	23.19 Å
Atom count	4132
Residues	543
Excluded volume	74142 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1gnl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1gnl__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	HYBRID CLUSTER PROTEIN
Molecular weight formula_weight	58595.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9885

SNAMFCYQCQETVGNKGCTQVGVCGKKPETAALQDALIYVTKGLGQIATRLRAEGKAVDHRIDRLVTGNLFATITNANFDDDILAERVRMTCAAKKELAASLTDKSGLSDAALWEASEKSAMLAKAGTVGVMATTDDDVRSLRWLITFGLKGMAAYAKHADVLGKHENSLDAFMQEALAKTLDDSLSVADLVALTLETGKFGVSAMALLDAANTGTYGHPEITKVNIGVGSNPGILISGHDLRDLEMLLKQTEGTGVDVYTHSEMLPAHYYPAFKKYAHFKGNYGNAWWKQKEEFESFNGPVLLTTNCLVPPKDSYKDRVYTTGIVGFTGCKHIPGEIGEHKDFSAIIAHAKTCPAPTEIESGEIIGGFAHNQVLALADKVIDAVKSGAIKKFVVMAGCDGRAKSRSYYTDFAEGLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLEDVNDLPIVYNIAWYEQKAVIVLLALLSLGVKNIHLGPTLPAFLSPNVAKVLVEQFNIGGITSPQDDLKAFFG

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR/OXYGEN HYBRID CLUSTER
Molecular weight formula_weight	367.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1562

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1gnla_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.1 — Hybrid cluster protein (prismane protein)

Domain ID domain_id	d1gnlb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.1 — Hybrid cluster protein (prismane protein)

CATH v4.4 (8 domains)

Domain ID domain_id	1gnlA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1gnlA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1gnlA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1gnlA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1gnlB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1gnlB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1gnlB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1gnlB04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

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Unit-cell length a length_a	57.330 Å
Unit-cell length b length_b	61.650 Å
Unit-cell length c length_c	72.250 Å
Unit-cell angle α angle_alpha	82.77 °
Unit-cell angle β angle_beta	73.67 °
Unit-cell angle γ angle_gamma	87.31 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	28.630 Å
R factor r_factor	0.1300
R_work r_work	0.1290
R_free r_free	0.1450

Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A

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

HYBRID CLUSTER PROTEIN

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

1gnl__assembly_1__model_1

1gnl__assembly_1__model_1 | I(q)

1gnl__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A

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

HYBRID CLUSTER PROTEIN

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

1gnl__assembly_1__model_1

1gnl__assembly_1__model_1 | I(q)

1gnl__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)