9ozd

Crystal structure of the polysaccharide lyase RbmB from Vibrio cholerae bound to Vibrio Polysaccharide

Method: X-RAY DIFFRACTION

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

Polysaccharide lyase

Vibrio cholerae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose ; × 1 SODIUM ION × 1 GLYCEROL × 5 FORMIC ACID × 3 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 2	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose ; × 1 ;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-{[(2R,3S,4R,5S,6R)-5-acetamido-3,4,6-trihydroxyoxane-2-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose ; × 1 SODIUM ION × 1 GLYCEROL × 4 FORMIC ACID × 1 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 2	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose ; × 1 ;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-{[(2R,3S,4R,5S,6R)-5-acetamido-3,4,6-trihydroxyoxane-2-carbonyl]amino}acetic acid (non-preferred name) ; × 1 SODIUM ION × 1 GLYCEROL × 2 FORMIC ACID × 1 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 1	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose ; × 1 SODIUM ION × 1 GLYCEROL × 2 FORMIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KTH3_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–380； UniProt 32–408 Author chain B； PDBConstruct 4–380； UniProt 32–408 Author chain C； PDBConstruct 4–380； UniProt 32–408 Author chain D； PDBConstruct 4–380； UniProt 32–408

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	9ozd
Deposition date deposition_date	2025-06-05
Structure title title	Crystal structure of the polysaccharide lyase RbmB from Vibrio cholerae bound to Vibrio Polysaccharide
Keywords keywords	polysaccharide lyase, beta-helix, periplasm, glycosidase, LYASE; LYASE
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.

9ozd__assembly_1__model_1

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

Download this curve (.dat)

9ozd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ozd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.58 Å
Rg (electron density)	21.76 Å
Total Rg	22.59 Å
Atom count	5755
Residues	366
Excluded volume	51683 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ozd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9ozd__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9ozd__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9ozd__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Description description	Polysaccharide lyase
Molecular weight formula_weight	42697.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	25213

GSTEVNSHNVIEYGAIANDGEDDSNAFQHALNQLNNGDALIIPTGEYQICKTLYLKEKNNIEIIGSINSKLKKCRSFNGEYLLHITYTQNLKIQGLSFEGLNNGDLKPLWGEQGVYLGSTKGTLVVQNQFARFGDAALRMTTASQDHSIPPGSMAIKVSHNHFEDCAQVTTTQATAGTEMHGTQDIIIDNNQFNACKLKLSARADTRGAKVINNQFENINGTSNEVSYYSDVYYSGNTFLNINGFAINIYPNSRTEQNVQWGNISIIGNTFDAIQQGIRLQSFSINDPNNQSIKNIQISDNTFENIYFGNEIESQYKAIIRTNSQDNLVSFEHVNITGNQYQLTPYSKFISIDHKSKLINIQNNERIYSDHYYIQHFIKD

Source Source

Source organism organism	Vibrio cholerae
NCBI taxonomy ID ncbi_taxonomy_id	948564
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose ;
Molecular weight formula_weight	760.6 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 branched

Description description	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-{[(2R,3S,4R,5S,6R)-5-acetamido-3,4,6-trihydroxyoxane-2-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose ;
Molecular weight formula_weight	1197.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;{[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-{[(2R,3S,4R,5S,6R)-5-acetamido-3,4,6-trihydroxyoxane-2-carbonyl]amino}acetic acid (non-preferred name) ;
Molecular weight formula_weight	1034.9 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 7 Entity 7 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1280

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Unit-cell length a length_a	123.555 Å
Unit-cell length b length_b	52.563 Å
Unit-cell length c length_c	133.229 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	33.420 Å
R factor r_factor	0.1699
R_work r_work	0.1678
R_free r_free	0.2094

Crystal structure of the polysaccharide lyase RbmB from Vibrio cholerae bound to Vibrio Polysaccharide

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

Polysaccharide lyase

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

9ozd__assembly_1__model_1

9ozd__assembly_1__model_1 | I(q)

9ozd__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (2)

Crystal structure of the polysaccharide lyase RbmB from Vibrio cholerae bound to Vibrio Polysaccharide

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

Polysaccharide lyase

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

9ozd__assembly_1__model_1

9ozd__assembly_1__model_1 | I(q)

9ozd__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (2)