SAXSdb — 7odj

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

Man5A

Cellvibrio mixtus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 4 ACETATE ION × 1 (1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6QT42_9GAMM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 2–432； UniProt 26–456

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	7odj
Deposition date deposition_date	2021-04-29
Structure title title	Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine
Keywords keywords	Mannosidase, covalent inhibitor, cyclophellitol, cellvibrio, 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.

7odj__assembly_1__model_1

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

Download this curve (.dat)

7odj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7odj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.86 Å
Rg (electron density)	19.54 Å
Total Rg	20.53 Å
Atom count	6470
Residues	409
Excluded volume	58636 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7odj__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Man5A
Molecular weight formula_weight	50230.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA
Atom count atom_count	7294

MVAESNSAVAPTANVATSPAHEHFVRVNGGHFELQGKPYVITGVNMWYAAYLGAPNEVGDRDRLAKELDNLKAIGVNNLRVLAVSEKSEINSAVKPAVTNGFGNYDETLLQGLDYLLVELAKRDMTVVLYFNNFWQWSGGMTQYMAWIEGEPVQDPNVTNEWEAFMAKSASFYRSEKAQQEYRKTLEKIITRVNSINGKAYVDDATIMSWQLANEPRPGNSQTTAEEKQIYIDWVHAAAAYIKTLDAHHLVSSGSEGEMGSVNDMQVFIDAHATPDIDYLTYHMWIRNWSWFDKTKPAETWPSAWEKAQNYMRAHIDVAKQLNKPLVLEEFGLDRDMGSYAMDSTTEYRDNYFRGVFELMLASLEQGEPSAGYNIWAWNGYGRTTRANYWWQEGDDFMGDPPQEEQGMYGVFDTDTSTIAIMKEFNARFQPKLEHHHHHH

Source Source

Source organism organism	Cellvibrio mixtus
NCBI taxonomy ID ncbi_taxonomy_id	39650
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
Molecular weight formula_weight	330.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	424

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Unit-cell length a length_a	91.815 Å
Unit-cell length b length_b	102.230 Å
Unit-cell length c length_c	50.680 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	68.403 Å
R factor r_factor	—
R_work r_work	0.1246
R_free r_free	0.1577

Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine

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

Man5A

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

7odj__assembly_1__model_1

7odj__assembly_1__model_1 | I(q)

7odj__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine

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

Man5A

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

7odj__assembly_1__model_1

7odj__assembly_1__model_1 | I(q)

7odj__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)