8yuh

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with allosamidin

Method: X-RAY DIFFRACTION

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

Chitinase B

Serratia marcescens

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 2	2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose × 2 GLYCEROL × 25 PHOSPHATE ION × 4 ACETATE ION × 27 ALLOSAMIZOLINE × 2 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 2	2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose × 2 GLYCEROL × 27 PHOSPHATE ION × 2 ACETATE ION × 21 ALLOSAMIZOLINE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHIB_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–500； UniProt 2–499 Author chain B； PDBConstruct 3–500； UniProt 2–499

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	8yuh
Deposition date deposition_date	2024-03-27
Last revision last_revision	2025-04-02
Structure title title	X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with allosamidin
Keywords keywords	glycoside hydrolase family 18 GH18 chitinase hexahistigine-tag allosamidin, 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.

8yuh__assembly_1__model_1

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

Download this curve (.dat)

8yuh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yuh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.80 Å
Rg (electron density)	23.81 Å
Total Rg	24.60 Å
Atom count	4282
Residues	499
Excluded volume	75714 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yuh__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8yuh__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 (7)

Entity 1 Entity 1 polymer

Description description	Chitinase B
Molecular weight formula_weight	56912.5 kDa
EC 编号 ec_number	3.2.1.14
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	10930

MDSTRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPAARTKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTIADGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKITNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPNADYWLVGCDECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRLAAAALEHHHHHH

Source Source

Source organism organism	Serratia marcescens
NCBI taxonomy ID ncbi_taxonomy_id	615
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	52

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	48

Entity 6 Entity 6 non-polymer

Description description	ALLOSAMIZOLINE
Molecular weight formula_weight	216.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1572

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Unit-cell length a length_a	97.850 Å
Unit-cell length b length_b	97.850 Å
Unit-cell length c length_c	196.678 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	tetragonal

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	47.590 Å
R factor r_factor	0.1538
R_work r_work	0.1536
R_free r_free	0.1699

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with allosamidin

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

Chitinase B

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

8yuh__assembly_1__model_1

8yuh__assembly_1__model_1 | I(q)

8yuh__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with allosamidin

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

Chitinase B

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

8yuh__assembly_1__model_1

8yuh__assembly_1__model_1 | I(q)

8yuh__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)