SAXSdb — 1mxi

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

Hypothetical tRNA/rRNA methyltransferase HI0766

Haemophilus influenzae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	IODIDE ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y766_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； 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	1mxi
Deposition date deposition_date	2002-10-02
Structure title title	Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot
Keywords keywords	methyltransferase, S-adenosylhomocysteine, spoU family, Structure 2 Function Project, S2F, Structural Genomics, 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.

1mxi__assembly_1__model_1

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

Download this curve (.dat)

1mxi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mxi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.05 Å
Rg (electron density)	19.18 Å
Total Rg	20.05 Å
Atom count	2574
Residues	312
Excluded volume	46107 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mxi__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 (4)

Entity 1 Entity 1 polymer

Description description	Hypothetical tRNA/rRNA methyltransferase HI0766
Molecular weight formula_weight	18427.4 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1479

MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	727
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1mxia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

CATH v4.4 (1 domains)

Domain ID domain_id	1mxiA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

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Unit-cell length a length_a	40.800 Å
Unit-cell length b length_b	40.800 Å
Unit-cell length c length_c	165.800 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1960
R_free r_free	0.2540

Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot

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

Hypothetical tRNA/rRNA methyltransferase HI0766

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

1mxi__assembly_1__model_1

1mxi__assembly_1__model_1 | I(q)

1mxi__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot

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

Hypothetical tRNA/rRNA methyltransferase HI0766

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

1mxi__assembly_1__model_1

1mxi__assembly_1__model_1 | I(q)

1mxi__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)