SAXSdb — 2dsl

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

Phenylacetic acid degradation protein PaaI

Thermus thermophilus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SJP3_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain B； PDBConstruct 1–136； UniProt 1–136

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	2dsl
Deposition date deposition_date	2006-06-30
Structure title title	Mutant N33D structure of phenylacetic acid degradation protein PaaI from Thermus thermophilus HB8
Keywords keywords	;THIOESTERASE, HOT DOG FOLD, PHENYLACETIC ACID DEGRADATION, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2dsl__assembly_1__model_1

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

Download this curve (.dat)

2dsl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dsl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.76 Å
Rg (electron density)	20.67 Å
Total Rg	21.61 Å
Atom count	3446
Residues	460
Excluded volume	61370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dsl__assembly_1__model_1`	tetrameric （4）	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	Phenylacetic acid degradation protein PaaI
Molecular weight formula_weight	14281.2 kDa
Mutation mutation	N33D
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	1957

MRDPFMEALGLKVLHLAPGEAVVAGEVRADHLDLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRLGGDGDDVPAGTGNLAPREA

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	233

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dsla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.5 — PaaI/YdiI-like

Domain ID domain_id	d2dslb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
Superfamily Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
Family Family family	d.38.1.5 — PaaI/YdiI-like

CATH v4.4 (2 domains)

Domain ID domain_id	2dslA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

Domain ID domain_id	2dslB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	10 — Hotdog Thioesterase

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Unit-cell length a length_a	57.670 Å
Unit-cell length b length_b	57.670 Å
Unit-cell length c length_c	139.696 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	16

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	22.560 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2150

Mutant N33D structure of phenylacetic acid degradation protein PaaI from Thermus thermophilus HB8

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

Phenylacetic acid degradation protein PaaI

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

2dsl__assembly_1__model_1

2dsl__assembly_1__model_1 | I(q)

2dsl__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Mutant N33D structure of phenylacetic acid degradation protein PaaI from Thermus thermophilus HB8

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

Phenylacetic acid degradation protein PaaI

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

2dsl__assembly_1__model_1

2dsl__assembly_1__model_1 | I(q)

2dsl__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)