SAXSdb — 4hmd

▼

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

Chitinase 60

Vibrio marinus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE × 2 SODIUM ION × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1VBB0_VIBMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–528； UniProt 23–550

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4hmd
Deposition date deposition_date	2012-10-18
Structure title title	Crystal structure of cold-adapted chitinase from Moritella marina with a reaction intermediate - oxazolinium ion (NGO)
Keywords keywords	Chitinase, hydrolaze, TIM-barrel, Ig-like, Immunoglobulin like domain, ChB D, Chitin binding domain, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4hmd__assembly_1__model_1

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

Download this curve (.dat)

4hmd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4hmd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.88 Å
Rg (electron density)	39.33 Å
Total Rg	39.29 Å
Atom count	8344
Residues	1056
Excluded volume	146860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4hmd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Chitinase 60
Molecular weight formula_weight	58617.4 kDa
EC 编号 ec_number	3.2.1.14
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	4340

GTITSQDDNVVVGYWHNWCDGRGYQGGNAPCVELKTVNPQYNVVNISFMKVYDIAEGRIPTFKLDPTIALSEAEFIAQIDTLNSQGRSVLIALGGADAHIELTRGDEDALAAEIIRLTDLYGFDGLDIDLEQAAITAKDNQFVIPAALKMVKEHYRKTGDNFMITMAPEFPYLTANGAYTPYLTELDGYYDFINPQFYNQGGDGLWIEGVGWIAQNNDALKEEFIYYIADSLINGTRNYHKIPHDKLVFGLPSNIDAAATGYIQDPQDLYKAFDRLKAQGQPLRGVMTWSVNWDMGTDAANNSYNQQFIKDYGNFIHNQLPPVTDMTPTLSGIVDTRVELDSHFDPLIGITAKDYQGNDITADVTVSGSVNTNQVGDYLLTYSVSSDDETTNQPRKITVYEILPAFTGITDTTVVIDSEFDPMQGVSASHPTQGDLTANITVTGEVDTNVVGVYELTYQLFYGQDNQQNMTDKRIVTVVTDAVSDDDWQVGSTYVKDDKVTHNGATWTAQWWTKGEEPGTTGEWGVWR

Source Source

Source organism organism	Vibrio marinus
Common name common_name	Moritella marina
NCBI taxonomy ID ncbi_taxonomy_id	90736
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4hmdA01
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	4hmdA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4hmdA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4hmdA04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	20 — Carbohydrate-binding module superfamily 5/12

▶

Unit-cell length a length_a	67.091 Å
Unit-cell length b length_b	67.091 Å
Unit-cell length c length_c	258.033 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	2.260 Å
Low-resolution limit resolution_low	43.170 Å
R factor r_factor	0.1887
R_work r_work	0.1856
R_free r_free	0.2481

Crystal structure of cold-adapted chitinase from Moritella marina with a reaction intermediate - oxazolinium ion (NGO)

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

Chitinase 60

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

4hmd__assembly_1__model_1

4hmd__assembly_1__model_1 | I(q)

4hmd__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of cold-adapted chitinase from Moritella marina with a reaction intermediate - oxazolinium ion (NGO)

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

Chitinase 60

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

4hmd__assembly_1__model_1

4hmd__assembly_1__model_1 | I(q)

4hmd__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)