2ze8

Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate

Method: X-RAY DIFFRACTION

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

Isopentenyl transferase

Agrobacterium tumefaciens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PYROPHOSPHATE 2- × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PYROPHOSPHATE 2- × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	PYROPHOSPHATE 2- × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	PYROPHOSPHATE 2- × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPTZ_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–243； UniProt 1–243 Author chain B； PDBConstruct 1–243； UniProt 1–243 Author chain C； PDBConstruct 1–243； UniProt 1–243 Author chain D； PDBConstruct 1–243； UniProt 1–243

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	2ze8
Deposition date deposition_date	2007-12-06
Structure title title	Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate
Keywords keywords	transferase, Crown gall tumor, Cytokinin biosynthesis; TRANSFERASE
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.

2ze8__assembly_1__model_1

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

Download this curve (.dat)

2ze8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ze8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.82 Å
Rg (electron density)	17.97 Å
Total Rg	18.74 Å
Atom count	1824
Residues	226
Excluded volume	32240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ze8__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ze8__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ze8__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ze8__assembly_4__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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ze8a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

Domain ID domain_id	d2ze8b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

Domain ID domain_id	d2ze8c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

Domain ID domain_id	d2ze8d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

CATH v4.4 (8 domains)

Domain ID domain_id	2ze8A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2ze8A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

Domain ID domain_id	2ze8B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2ze8B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

Domain ID domain_id	2ze8C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2ze8C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

Domain ID domain_id	2ze8D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2ze8D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

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Unit-cell length a length_a	97.510 Å
Unit-cell length b length_b	97.568 Å
Unit-cell length c length_c	131.108 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	131.310 Å
R factor r_factor	0.2339
R_work r_work	0.2303
R_free r_free	0.3022

Description description	Isopentenyl transferase
Molecular weight formula_weight	28842.8 kDa
EC 编号 ec_number	2.5.1.27
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7296

Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate

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

Isopentenyl transferase

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

2ze8__assembly_1__model_1

2ze8__assembly_1__model_1 | I(q)

2ze8__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Agrobacterium tumefaciens
NCBI taxonomy ID ncbi_taxonomy_id	358
Host organism host_organism	Escherichia coli

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	4

Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate

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

Isopentenyl transferase

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

2ze8__assembly_1__model_1

2ze8__assembly_1__model_1 | I(q)

2ze8__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)