SAXSdb — 1ppw

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

Isopentenyl-diphosphate delta-isomerase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 MAGNESIUM ION × 2 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IDI_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–182； UniProt 1–182 Author chain B； PDBConstruct 1–182； UniProt 1–182

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	1ppw
Deposition date deposition_date	2003-06-17
Structure title title	ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE IN COMPLEX WITH THE BROMOHYDRINE OF IPP
Keywords keywords	COMPLEX, 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.

1ppw__assembly_1__model_1

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

Download this curve (.dat)

1ppw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ppw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.50 Å
Rg (electron density)	21.84 Å
Total Rg	22.63 Å
Atom count	2854
Residues	356
Excluded volume	50415 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ppw__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 (5)

Entity 1 Entity 1 polymer

Description description	Isopentenyl-diphosphate delta-isomerase
Molecular weight formula_weight	20644.4 kDa
EC 编号 ec_number	5.3.3.2
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	3041

MQTEHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQLKL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE
Molecular weight formula_weight	264.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ppwa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.2 — IPP isomerase-like

Domain ID domain_id	d1ppwb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.2 — IPP isomerase-like

Domain ID domain_id	d1ppwb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1ppwA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	1ppwB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

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Unit-cell length a length_a	69.090 Å
Unit-cell length b length_b	71.880 Å
Unit-cell length c length_c	91.730 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	2.210 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2023
R_work r_work	0.1762
R_free r_free	0.2530

ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE IN COMPLEX WITH THE BROMOHYDRINE OF IPP

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

1ppw__assembly_1__model_1

1ppw__assembly_1__model_1 | I(q)

1ppw__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE IN COMPLEX WITH THE BROMOHYDRINE OF IPP

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

1ppw__assembly_1__model_1

1ppw__assembly_1__model_1 | I(q)

1ppw__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)