SAXSdb — 3vkj

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

Isopentenyl-diphosphate delta-isomerase

Sulfolobus shibatae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IDI2_SULSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–368； UniProt 1–368 Author chain B； PDBConstruct 1–368； UniProt 1–368 Author chain C； PDBConstruct 1–368； UniProt 1–368 Author chain D； PDBConstruct 1–368； UniProt 1–368

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	3vkj
Deposition date deposition_date	2011-11-17
Structure title title	Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form
Keywords keywords	type 2 isopentenyl diphosphate isomerase, ISOMERASE; ISOMERASE
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.

3vkj__assembly_1__model_1

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

Download this curve (.dat)

3vkj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vkj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.48 Å
Rg (electron density)	42.78 Å
Total Rg	43.21 Å
Atom count	22648
Residues	2904
Excluded volume	408470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vkj__assembly_1__model_1`	octameric （8）	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 (3)

Entity 1 Entity 1 polymer

Description description	Isopentenyl-diphosphate delta-isomerase
Molecular weight formula_weight	40475.8 kDa
EC 编号 ec_number	5.3.3.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12048

MPDIVNRKVEHVEIAAFENVDGLSSSTFLNDVILVHQGFPGISFSEINTKTKFFRKEISVPVMVTGMTGGRNELGRINKIIAEVAEKFGIPMGVGSQRVAIEKAEARESFAIVRKVAPTIPIIANLGMPQLVKGYGLKEFQDAIQMIEADAIAVHLNPAQEVFQPEGEPEYQIYALEKLRDISKELSVPIIVKESGNGISMETAKLLYSYGIKNFDTSGQGGTNWIAIEMIRDIRRGNWKAESAKNFLDWGVPTAASIMEVRYSVPDSFLVGSGGIRSGLDAAKAIALGADIAGMALPVLKSAIEGKESLEQFFRKIIFELKAAMMLTGSKDVDALKKTSIVILGKLKEWAEYRGINLSIYEKVRKRE

Source Source

Source organism organism	Sulfolobus shibatae
NCBI taxonomy ID ncbi_taxonomy_id	2286
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
Molecular weight formula_weight	458.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	724

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3vkjA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3vkjB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3vkjC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3vkjD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	100.841 Å
Unit-cell length b length_b	100.841 Å
Unit-cell length c length_c	336.651 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	35.150 Å
R factor r_factor	0.1864
R_work r_work	0.1850
R_free r_free	0.2170

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form

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

Isopentenyl-diphosphate delta-isomerase

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

3vkj__assembly_1__model_1

3vkj__assembly_1__model_1 | I(q)

3vkj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form

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

Isopentenyl-diphosphate delta-isomerase

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

3vkj__assembly_1__model_1

3vkj__assembly_1__model_1 | I(q)

3vkj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)