SAXSdb — 4dhv

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

Ferredoxin

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SILVER/IRON/SULFUR CLUSTER × 2 COBALT HEXAMMINE(III) × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FER_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–66； UniProt 2–67 Author chain B； PDBConstruct 1–66； UniProt 2–67

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	4dhv
Deposition date deposition_date	2012-01-30
Structure title title	Crystal structure of the Pyrococcus furiosus ferredoxin D14C variant containing the heterometallic [AgFe3S4] cluster
Keywords keywords	;ferredoxin, Pyrococcus furiosus, iron-sulfur protein, electron transport, heterometallic, [AgFe3S4] cluster, silver, artificial metalloprotein ;; ELECTRON TRANSPORT
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.

4dhv__assembly_1__model_1

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

Download this curve (.dat)

4dhv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dhv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.77 Å
Rg (electron density)	15.80 Å
Total Rg	16.83 Å
Atom count	1026
Residues	131
Excluded volume	18412 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dhv__assembly_1__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	Ferredoxin
Molecular weight formula_weight	7159.1 kDa
Mutation mutation	D14C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	1186

AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SILVER/IRON/SULFUR CLUSTER
Molecular weight formula_weight	403.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	COBALT HEXAMMINE(III)
Molecular weight formula_weight	161.1 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	98

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4dhva_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.4 — Single 4Fe-4S cluster ferredoxin

Domain ID domain_id	d4dhvb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.4 — Single 4Fe-4S cluster ferredoxin

CATH v4.4 (2 domains)

Domain ID domain_id	4dhvA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4dhvB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	45.110 Å
Unit-cell length b length_b	49.330 Å
Unit-cell length c length_c	54.390 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	24.660 Å
R factor r_factor	0.1910
R_work r_work	0.1880
R_free r_free	0.2470

Crystal structure of the Pyrococcus furiosus ferredoxin D14C variant containing the heterometallic [AgFe3S4] cluster

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

Ferredoxin

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

4dhv__assembly_1__model_1

4dhv__assembly_1__model_1 | I(q)

4dhv__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the Pyrococcus furiosus ferredoxin D14C variant containing the heterometallic [AgFe3S4] cluster

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

Ferredoxin

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

4dhv__assembly_1__model_1

4dhv__assembly_1__model_1 | I(q)

4dhv__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)