SAXSdb — 3dnf

▼

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

4-hydroxy-3-methylbut-2-enyl diphosphate reductase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE3-S4 CLUSTER × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPH_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–289； UniProt 1–289 Author chain B； PDBConstruct 1–289； UniProt 1–289

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3dnf
Deposition date deposition_date	2008-07-02
Structure title title	Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway
Keywords keywords	trilobal strucure, open alpha/beta, Iron, Iron-sulfur, Isoprene biosynthesis, Metal-binding, NADP, Oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3dnf__assembly_1__model_1

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

Download this curve (.dat)

3dnf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dnf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.93 Å
Rg (electron density)	32.96 Å
Total Rg	33.12 Å
Atom count	4438
Residues	563
Excluded volume	79746 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dnf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Molecular weight formula_weight	33220.1 kDa
EC 编号 ec_number	1.17.1.2
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	5076

MVDIIIAEHAGFCFGVKRAVKLAEESLKESQGKVYTLGPIIHNPQEVNRLKNLGVFPSQGEEFKEGDTVIIRSHGIPPEKEEALRKKGLKVIDATCPYVKAVHEAVCQLTREGYFVVLVGEKNHPEVIGTLGYLRACNGKGIVVETLEDIGEALKHERVGIVAQTTQNEEFFKEVVGEIALWVKEVKVINTICNATSLRQESVKKLAPEVDVMIIIGGKNSGNTRRLYYISKELNPNTYHIETAEELQPEWFRGVKRVGISAGASTPDWIIEQVKSRIQEICEGQLVSSRSHHHHHH

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

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	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	561

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3dnfa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.155 — LytB-like
Superfamily Superfamily superfamily	c.155.1 — LytB-like
Family Family family	c.155.1.1 — LytB-like

Domain ID domain_id	d3dnfb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.155 — LytB-like
Superfamily Superfamily superfamily	c.155.1 — LytB-like
Family Family family	c.155.1.1 — LytB-like

CATH v4.4 (6 domains)

Domain ID domain_id	3dnfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	20 — 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain

Domain ID domain_id	3dnfA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11270 —

Domain ID domain_id	3dnfA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	20 — 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain

Domain ID domain_id	3dnfB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	20 — 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain

Domain ID domain_id	3dnfB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11270 —

Domain ID domain_id	3dnfB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	20 — 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain

▶

Unit-cell length a length_a	60.370 Å
Unit-cell length b length_b	87.760 Å
Unit-cell length c length_c	72.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	9.900 Å
R factor r_factor	0.1943
R_work r_work	0.1926
R_free r_free	0.2261

Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway

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

4-hydroxy-3-methylbut-2-enyl diphosphate reductase

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

3dnf__assembly_1__model_1

3dnf__assembly_1__model_1 | I(q)

3dnf__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) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway

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

4-hydroxy-3-methylbut-2-enyl diphosphate reductase

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

3dnf__assembly_1__model_1

3dnf__assembly_1__model_1 | I(q)

3dnf__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) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)