SAXSdb — 8yvw

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

(S)-2-haloacid dehalogenase

Pseudomonas sp. A2C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FORMIC ACID × 2 IMIDAZOLE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2Z3V8_9PSED
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–240； UniProt 1–240

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	8yvw
Deposition date deposition_date	2024-03-29
Last revision last_revision	2024-05-08
Structure title title	Crystal structure of D12N mutant of L-azetidine-2-carboxylate hydrolase
Keywords keywords	azetidine-2-carboxylate, dehalogenase, alpha/beta hydrolase, 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.

8yvw__assembly_1__model_1

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

Download this curve (.dat)

8yvw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yvw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.70 Å
Rg (electron density)	17.68 Å
Total Rg	18.72 Å
Atom count	1927
Residues	240
Excluded volume	34102 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yvw__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	(S)-2-haloacid dehalogenase
Molecular weight formula_weight	27145.6 kDa
EC 编号 ec_number	3.8.1.2
Mutation mutation	D12N
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	2561

MQLTDFKALTFNCYGTLIDWETGIVNALQPLAKRTGKTFTSDELLEVFGRNESPQQTETPGALYQDILRAVYDRIAKEWGLEPDAAEREEFGTSVKNWPAFPDTVEALQYLKKHYKLVILSNIDRNEFKLSNAKLGVEFDHIITAQDVGSYKPNPNNFTYMIDALAKAGIEKKDILHTAESLYHDHIPANDAGLVSAWIYRRHGKEGYGATHVPSRMPNVDFRFNSMGEMAEAHKQALKG

Source Source

Source organism organism	Pseudomonas sp. A2C
NCBI taxonomy ID ncbi_taxonomy_id	533317
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	485

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Unit-cell length a length_a	47.176 Å
Unit-cell length b length_b	71.361 Å
Unit-cell length c length_c	72.349 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.190 Å
Low-resolution limit resolution_low	20.380 Å
R factor r_factor	0.1199
R_work r_work	0.1186
R_free r_free	0.1450

Crystal structure of D12N mutant of L-azetidine-2-carboxylate hydrolase

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

(S)-2-haloacid dehalogenase

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

8yvw__assembly_1__model_1

8yvw__assembly_1__model_1 | I(q)

8yvw__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)

Crystal structure of D12N mutant of L-azetidine-2-carboxylate hydrolase

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

(S)-2-haloacid dehalogenase

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

8yvw__assembly_1__model_1

8yvw__assembly_1__model_1 | I(q)

8yvw__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)