SAXSdb — 2d0d

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

2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase

Pseudomonas fluorescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 PHOSPHATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P96965_PSEFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–282； UniProt 1–282

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	2d0d
Deposition date deposition_date	2005-08-01
Structure title title	Crystal Structure of a Meta-cleavage Product Hydrolase (CumD) A129V Mutant
Keywords keywords	;alpha/beta-hydrolase, beta-ketolase, meta-cleavage product hydrolase, substrate specificity, cumene degradation, polychlorinated biphenyl degradation, PCB, 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.

2d0d__assembly_1__model_1

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

Download this curve (.dat)

2d0d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d0d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.49 Å
Rg (electron density)	25.77 Å
Total Rg	26.45 Å
Atom count	4306
Residues	542
Excluded volume	76015 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d0d__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
Molecular weight formula_weight	31550.7 kDa
EC 编号 ec_number	3.7.1.9
Mutation mutation	A129V
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	2525

MANLEIGKSILAAGVLTNYHDVGEGQPVILIHGSGPGVSAYANWRLTIPALSKFYRVIAPDMVGFGFTDRPENYNYSKDSWVDHIIGIMDALEIEKAHIVGNSFGGGLAIATALRYSERVDRMVLMGAVGTRFDVTEGLNAVWGYTPSIENMRNLLDIFAYDRSLVTDELARLRYEASIQPGFQESFSSMFPEPRQRWIDALASSDEDIKTLPNETLIIHGREDQVVPLSSSLRLGELIDRAQLHVFGRCGHWTQIEQTDRFNRLVVEFFNEANTPKLVGRP

Source Source

Source organism organism	Pseudomonas fluorescens
NCBI taxonomy ID ncbi_taxonomy_id	294
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	372

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2d0da_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.10 — Carbon-carbon bond hydrolase

CATH v4.4 (1 domains)

Domain ID domain_id	2d0dA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	76.650 Å
Unit-cell length b length_b	116.623 Å
Unit-cell length c length_c	78.640 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	46.840 Å
R factor r_factor	0.1730
R_work r_work	0.1730
R_free r_free	0.1910

Crystal Structure of a Meta-cleavage Product Hydrolase (CumD) A129V Mutant

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

2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase

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

2d0d__assembly_1__model_1

2d0d__assembly_1__model_1 | I(q)

2d0d__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (3)

Crystal Structure of a Meta-cleavage Product Hydrolase (CumD) A129V Mutant

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

2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase

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

2d0d__assembly_1__model_1

2d0d__assembly_1__model_1 | I(q)

2d0d__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (3)