SAXSdb — 2zm5

▼

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

tRNA delta(2)-isopentenylpyrophosphate transferase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	tRNA(Phe) × 1 MAGNESIUM ION × 6 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	tRNA(Phe) × 1 MAGNESIUM ION × 1 water × 2	Consistent with all polymers
3	Protein–RNA	Homooligomer	Protein 2 RNA 2	tRNA(Phe) × 2 MAGNESIUM ION × 7 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MIAA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–316； UniProt 1–316 Author chain B； PDBConstruct 1–316； UniProt 1–316

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	2zm5
Deposition date deposition_date	2008-04-11
Structure title title	Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)
Keywords keywords	;PROTEIN-RNA COMPLEX, tRNA modification enzyme, Nucleotide-binding, Nucleotidyltransferase, Transferase, tRNA processing, TRANSFERASE-RNA COMPLEX ;; TRANSFERASE/RNA
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.

2zm5__assembly_1__model_1

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

Download this curve (.dat)

2zm5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zm5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.06 Å
Rg (electron density)	28.56 Å
Total Rg	29.05 Å
Atom count	3986
Residues	373
Excluded volume	65320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zm5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zm5__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zm5__assembly_3__model_1`	tetrameric （4）	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	tRNA delta(2)-isopentenylpyrophosphate transferase
Molecular weight formula_weight	35482.3 kDa
EC 编号 ec_number	2.5.1.8
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	8015

MSDISKASLPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVVGAIAG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	tRNA(Phe)
Molecular weight formula_weight	24485.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D

GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCACCA

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	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	162

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2zm5A01
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	2zm5A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2zm5B01
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

▶

Unit-cell length a length_a	88.200 Å
Unit-cell length b length_b	89.400 Å
Unit-cell length c length_c	150.800 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	2.550 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2400
R_work r_work	0.2400
R_free r_free	0.2700

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)

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

tRNA delta(2)-isopentenylpyrophosphate 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

2zm5__assembly_1__model_1

2zm5__assembly_1__model_1 | I(q)

2zm5__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)

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

tRNA delta(2)-isopentenylpyrophosphate 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

2zm5__assembly_1__model_1

2zm5__assembly_1__model_1 | I(q)

2zm5__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)