2vkr

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

Method: X-RAY DIFFRACTION

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

ZINC-CONTAINING FERREDOXIN

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	FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 ZINC ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 ZINC ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 ZINC ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 ZINC ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 ZINC ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FER_ACIAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–103； UniProt 1–103 Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain C； PDBConstruct 1–103； UniProt 1–103 Author chain D； PDBConstruct 1–103； UniProt 1–103 Author chain E； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103 Author chain G； PDBConstruct 1–103； UniProt 1–103

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	2vkr
Deposition date deposition_date	2007-12-23
Structure title title	3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin
Keywords keywords	;ZINC, IRON, 3FE-4S, 4FE-4S, TRANSPORT, ZN CENTER, HEMIHEDRIC TWINNIG, IRON-SULFUR PROTEIN, FERREDOXIN, METHYLATION, THERMOPHILE, IRON-SULFUR, THERMOSTABLE PROTEIN, METAL-BINDING, PROTEIN FOLDING, ELECTRON 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.

2vkr__assembly_2__model_1

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

Download this curve (.dat)

2vkr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vkr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	13.05 Å
Rg (electron density)	12.13 Å
Total Rg	13.18 Å
Atom count	786
Residues	103
Excluded volume	14115 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vkr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vkr__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2vkr__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2vkr__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2vkr__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2vkr__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2vkr__assembly_7__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	ZINC-CONTAINING FERREDOXIN
Molecular weight formula_weight	11014.6 kDa
Source method src_method	nat
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	5616

GIDPNYRTSRQVVGEHQGHKVYGPVDPPKVLGIHGTIVGVDFDLCIADGSCITACPVNVFQWYDTPGHPASEKKADPINEQACIFCMACVNVCPVAAIDVKPP

Entity 2 Entity 2 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	7

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	7

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2vkra_
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.58.1.3 — Archaeal ferredoxins

Domain ID domain_id	d2vkrb_
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.58.1.3 — Archaeal ferredoxins

Domain ID domain_id	d2vkrc_
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.58.1.3 — Archaeal ferredoxins

Domain ID domain_id	d2vkrd_
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.58.1.3 — Archaeal ferredoxins

Domain ID domain_id	d2vkre_
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.58.1.3 — Archaeal ferredoxins

Domain ID domain_id	d2vkrf_
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.58.1.3 — Archaeal ferredoxins

Domain ID domain_id	d2vkrg_
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.58.1.3 — Archaeal ferredoxins

CATH v4.4 (7 domains)

Domain ID domain_id	2vkrA00
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	2vkrB00
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	2vkrC00
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	2vkrD00
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	2vkrE00
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	2vkrF00
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	2vkrG00
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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7. Citations (6)

Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.

FEBS Lett. (2008)

PMID: 18258200 · DOI: 10.1016/j.febslet.2008.01.041 PRIMARY

A Spectroscopic Study of the Temperature Induced Modifications on Ferredoxin Folding and Iron-Sulfur Moieties

Biochemistry (2007)

PMID: 17696500 · DOI: 10.1021/BI700967G

;Studies of the Molten Globule State of Ferredoxin: Structural Characterisation and Implications on Protein Folding and Iron-Sulfur Centre Assembly ;

Proteins: Struct.,Funct., Genet. (2007)

PMID: 17510960 · DOI: 10.1002/PROT.21448

;Natural Domain Design: Enhanced Thermal Stability of a Zinc Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site ;

Biochemistry (2006)

PMID: 16922514 · DOI: 10.1021/BI0610698

,Di-Cluster, Seven-Iron Ferredoxins from Hyperthermophilic Sulfolobales

J.Biol.Inorg.Chem. (1998)

A Seven Iron Ferredoxin from the Thermoacidophilic Archaeon Desulfurolobus Ambivalens

Eur.J.Biochem. (1995)

PMID: 7851403 · DOI: 10.1111/J.1432-1033.1995.TB20392.X

Unit-cell length a length_a	117.500 Å
Unit-cell length b length_b	117.500 Å
Unit-cell length c length_c	50.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	21

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	19.480 Å
R factor r_factor	0.2196
R_work r_work	—
R_free r_free	0.2729

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

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

ZINC-CONTAINING 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

2vkr__assembly_2__model_1

2vkr__assembly_2__model_1 | I(q)

2vkr__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 (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) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (6)

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

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

ZINC-CONTAINING 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

2vkr__assembly_2__model_1

2vkr__assembly_2__model_1 | I(q)

2vkr__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 (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) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (6)