SAXSdb — 2z8q

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

Ferredoxin

Pyrococcus furiosus DSM 3638

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 COBALT HEXAMMINE(III) × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 1 COBALT HEXAMMINE(III) × 2 water × 1	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	2z8q
Deposition date deposition_date	2007-09-07
Structure title title	ferredoxin from Pyrococcus furiosus, D14C variant
Keywords keywords	ferredoxin iron-sulfur cluster, pyrococcus furiosus, two molecules in asymmetric unit, Electron transport, Metal-binding, Transport; 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.

2z8q__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2z8q__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2z8q__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	12.48 Å
Rg (electron density)	11.20 Å
Total Rg	12.44 Å
Atom count	516
Residues	66
Excluded volume	9250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2z8q__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2z8q__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 (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	A,B
Atom count atom_count	1248

AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA

Source Source

Source organism organism	Pyrococcus furiosus DSM 3638
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli BL21(DE3)

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	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	155

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2z8qa_
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	d2z8qb_
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	2z8qA00
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	2z8qB00
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	51.400 Å
Unit-cell length b length_b	116.800 Å
Unit-cell length c length_c	47.700 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	1.700 Å
Low-resolution limit resolution_low	26.010 Å
R factor r_factor	0.1656
R_work r_work	0.1641
R_free r_free	0.1940

ferredoxin from Pyrococcus furiosus, D14C variant

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

2z8q__assembly_2__model_1

2z8q__assembly_2__model_1 | I(q)

2z8q__assembly_2__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)

ferredoxin from Pyrococcus furiosus, D14C variant

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

2z8q__assembly_2__model_1

2z8q__assembly_2__model_1 | I(q)

2z8q__assembly_2__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)