SAXSdb — 2oym

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

Endoglycoceramidase II

Rhodococcus sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 N-{[(2R,3R,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PYRROLIDIN-2-YL]METHYL}-4-(DIMETHYLAMINO)BENZAMIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 N-{[(2R,3R,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PYRROLIDIN-2-YL]METHYL}-4-(DIMETHYLAMINO)BENZAMIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O33853_RHOSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–481； UniProt 31–490 Author chain B； PDBConstruct 22–481； UniProt 31–490

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	2oym
Deposition date deposition_date	2007-02-22
Structure title title	Endo-glycoceramidase II from Rhodococcus sp.: five-membered iminocyclitol complex
Keywords keywords	(alpha/beta)8 (TIM) barrel, Hydrolase; HYDROLASE
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.

2oym__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2oym__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oym__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.39 Å
Rg (electron density)	21.31 Å
Total Rg	22.21 Å
Atom count	3390
Residues	434
Excluded volume	59665 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oym__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2oym__assembly_2__model_1`	monomeric （1）	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	Endoglycoceramidase II
Molecular weight formula_weight	52122.5 kDa
EC 编号 ec_number	3.2.1.123
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	7494

MGSSHHHHHHSSGLVPRGSHMSGSGSGSGTALTPSYLKDDDGRSLILRGFNTASSAKSAPDGMPQFTEADLAREYADMGTNFVRFLISWRSVEPAPGVYDQQYLDRVEDRVGWYAERGYKVMLDMHQDVYSGAITPEGNSGNGAGAIGNGAPAWATYMDGLPVEPQPRWELYYIQPGVMRAFDNFWNTTGKHPELVEHYAKAWRAVADRFADNDAVVAYDLMNEPFGGSLQGPAFEAGPLAAMYQRTTDAIRQVDQDTWVCVAPQAIGVNQGLPSGLTKIDDPRAGQQRIAYCPHLYPLPLDIGDGHEGLARTLTDVTIDAWRANTAHTARVLGDVPIILGEFGLDTTLPGARDYIERVYGTAREMGAGVSYWSSDPGPWGPYLPDGTQTLLVDTLNKPYPRAVAGTPTEWSSTSDRLQLTIEPDAAITAPTEIYLPEAGFPGDVHVEGADVVGWDRQSRLLTVRTPADSGNVTVTVTPAA

Source Source

Source organism organism	Rhodococcus sp.
NCBI taxonomy ID ncbi_taxonomy_id	1831
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	N-{[(2R,3R,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PYRROLIDIN-2-YL]METHYL}-4-(DIMETHYLAMINO)BENZAMIDE
Molecular weight formula_weight	309.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	675

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2oymA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	2oymA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2oymB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	2oymB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

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Unit-cell length a length_a	53.786 Å
Unit-cell length b length_b	93.282 Å
Unit-cell length c length_c	94.471 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	18.300 Å
R factor r_factor	0.1820
R_work r_work	0.1800
R_free r_free	0.2120

Endo-glycoceramidase II from Rhodococcus sp.: five-membered iminocyclitol complex

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

Endoglycoceramidase II

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

2oym__assembly_2__model_1

2oym__assembly_2__model_1 | I(q)

2oym__assembly_2__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Endo-glycoceramidase II from Rhodococcus sp.: five-membered iminocyclitol complex

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

Endoglycoceramidase II

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

2oym__assembly_2__model_1

2oym__assembly_2__model_1 | I(q)

2oym__assembly_2__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)