SAXSdb — 7d51

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

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

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

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 1–160； UniProt 1–160 Author chain B； PDBConstruct 1–160； UniProt 1–160

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	7d51
Deposition date deposition_date	2020-09-24
Structure title title	Crystal structure of a truly knotted protein: cyclized YibK from Haemophilus influenzae
Keywords keywords	Topologically knotted protein, cyclized protein, SPOUT, trefoil knot, TRANSFERASE; 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.

7d51__assembly_1__model_1

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

Download this curve (.dat)

7d51__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d51__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.40 Å
Rg (electron density)	19.39 Å
Total Rg	20.24 Å
Atom count	2518
Residues	327
Excluded volume	44958 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d51__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	60.738 Å
Unit-cell length b length_b	68.781 Å
Unit-cell length c length_c	84.357 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	2.680 Å
Low-resolution limit resolution_low	26.670 Å
R factor r_factor	0.2398
R_work r_work	0.2367
R_free r_free	0.3011

Description description	;tRNA (cytidine(34)-2'-O)-methyltransferase ;
Molecular weight formula_weight	19183.2 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	2558

Crystal structure of a truly knotted protein: cyclized YibK from Haemophilus influenzae

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

;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

7d51__assembly_1__model_1

7d51__assembly_1__model_1 | I(q)

7d51__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 (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
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	40

Crystal structure of a truly knotted protein: cyclized YibK from Haemophilus influenzae

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

;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

7d51__assembly_1__model_1

7d51__assembly_1__model_1 | I(q)

7d51__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)