SAXSdb — 2ybo

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

METHYLTRANSFERASE

PSEUDOMONAS AERUGINOSA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 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	P95417_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–286； UniProt 1–279

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	2ybo
Deposition date deposition_date	2011-03-08
Structure title title	The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH
Keywords keywords	SUMT, TRANSFERASE, NIRE, HEME D1 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.

2ybo__assembly_1__model_1

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

Download this curve (.dat)

2ybo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ybo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.03 Å
Rg (electron density)	21.58 Å
Total Rg	22.49 Å
Atom count	3768
Residues	496
Excluded volume	67199 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ybo__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 (3)

Entity 1 Entity 1 polymer

Description description	METHYLTRANSFERASE
Molecular weight formula_weight	31402.0 kDa
EC 编号 ec_number	2.1.1.107
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	2085

AMADIGSMNTTVIPPSLLDVDFPAGSVALVGAGPGDPGLLTLRAWALLQQAEVVVYDRLVARELIALLPESCQRIYVGKRCGHHSLPQEEINELLVRLARQQRRVVRLKGGDPFIFGRGAEELERLLEAGVDCQVVPGVTAASGCSTYAGIPLTHRDLAQSCTFVTGHLQNDGRLDLDWAGLARGKQTLVFYMGLGNLAEIAARLVEHGLASDTPAALVSQGTQAGQQVTRGALAELPALARRYQLKPPTLIVVGQVVALFAERAMAHPSYLGAGSPVSREAVACALEHHHHHH

Source Source

Source organism organism	PSEUDOMONAS AERUGINOSA
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	195

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2yboa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.90 — Tetrapyrrole methylase
Superfamily Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
Family Family family	c.90.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2yboA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

Domain ID domain_id	2yboA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

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Unit-cell length a length_a	60.900 Å
Unit-cell length b length_b	115.100 Å
Unit-cell length c length_c	76.800 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	26.915 Å
R factor r_factor	0.2380
R_work r_work	0.2349
R_free r_free	0.2868

The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH

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

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

2ybo__assembly_1__model_1

2ybo__assembly_1__model_1 | I(q)

2ybo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH

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

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

2ybo__assembly_1__model_1

2ybo__assembly_1__model_1 | I(q)

2ybo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)