SAXSdb — 6ahw

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

;circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase ;

Haemophilus influenzae Rd KW20

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRML_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–80； UniProt 82–160 Author chain A； PDBConstruct 83–163； UniProt 1–81 Author chain B； PDBConstruct 2–80； UniProt 82–160 Author chain B； PDBConstruct 83–163； UniProt 1–81

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	6ahw
Deposition date deposition_date	2018-08-20
Structure title title	Crystal structure of circular-permutated YibK methyltransferase from Haemophilus influenzae
Keywords keywords	transferase, methyltransferase, circular permutation; 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.

6ahw__assembly_1__model_1

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

Download this curve (.dat)

6ahw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ahw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.73 Å
Rg (electron density)	19.68 Å
Total Rg	20.68 Å
Atom count	2604
Residues	324
Excluded volume	46710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ahw__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 (2)

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Unit-cell length a length_a	131.716 Å
Unit-cell length b length_b	46.941 Å
Unit-cell length c length_c	55.703 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.560 Å
Low-resolution limit resolution_low	29.850 Å
R factor r_factor	0.1953
R_work r_work	0.1935
R_free r_free	0.2287

Description description	;circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase ;
Molecular weight formula_weight	18702.7 kDa
EC 编号 ec_number	2.1.1.207
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2834

Crystal structure of circular-permutated YibK methyltransferase from Haemophilus influenzae

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

;circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase ;

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

6ahw__assembly_1__model_1

6ahw__assembly_1__model_1 | I(q)

6ahw__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 water

7. Citations (1)

Source organism organism	Haemophilus influenzae Rd KW20
NCBI taxonomy ID ncbi_taxonomy_id	71421
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

Crystal structure of circular-permutated YibK methyltransferase from Haemophilus influenzae

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

;circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase ;

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

6ahw__assembly_1__model_1

6ahw__assembly_1__model_1 | I(q)

6ahw__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 water

7. Citations (1)