SAXSdb — 3h3l

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

PUTATIVE SUGAR HYDROLASE

Parabacteroides distasonis ATCC 8503

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6LFX0_PARD8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–241； UniProt 31–270 Author chain B； PDBConstruct 2–241； UniProt 31–270 Author chain C； PDBConstruct 2–241； UniProt 31–270

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	3h3l
Deposition date deposition_date	2009-04-16
Structure title title	Crystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) from Parabacteroides distasonis ATCC 8503 at 1.59 A resolution
Keywords keywords	;YP_001304206.1, PUTATIVE SUGAR HYDROLASE, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Domain of Unknown Function (DUF1080), unknown function, 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.

3h3l__assembly_1__model_1

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

Download this curve (.dat)

3h3l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3h3l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.37 Å
Rg (electron density)	24.80 Å
Total Rg	25.36 Å
Atom count	3688
Residues	450
Excluded volume	65552 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3h3l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3h3l__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	PUTATIVE SUGAR HYDROLASE
Molecular weight formula_weight	27682.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6134

GAGTQTAQTQALDSDGIPTGGEWITMFDGKTLNGWRGYCRQDVPLGWVVEDGSITYKGSDNKADTGFGDLIYDKKFKNFVFEIEWKIDKAGNSGIFYTAQEIEGTPIYYSSPEYQLLDNENMPDAWEGCDGNRQAGAVYDMIMPDPQPVKPYGNWNKTRIVVYNQRVIHYMNDVKILEFQFGTPVWRALVDHSKFSKFSTSPEKCPEAYDLMLQCGKQPGYIGMQDHGYGVCFRNIRIKEL

Source Source

Source organism organism	Parabacteroides distasonis ATCC 8503
NCBI taxonomy ID ncbi_taxonomy_id	435591
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	488

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3h3lA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	560 — Exo-inulinase; domain 1

Domain ID domain_id	3h3lB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	560 — Exo-inulinase; domain 1

Domain ID domain_id	3h3lC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	560 — Exo-inulinase; domain 1

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Unit-cell length a length_a	117.259 Å
Unit-cell length b length_b	117.259 Å
Unit-cell length c length_c	118.068 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.590 Å
Low-resolution limit resolution_low	29.311 Å
R factor r_factor	0.1700
R_work r_work	0.1700
R_free r_free	0.1850

Crystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) from Parabacteroides distasonis ATCC 8503 at 1.59 A resolution

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

PUTATIVE SUGAR 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

3h3l__assembly_1__model_1

3h3l__assembly_1__model_1 | I(q)

3h3l__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) from Parabacteroides distasonis ATCC 8503 at 1.59 A resolution

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

PUTATIVE SUGAR 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

3h3l__assembly_1__model_1

3h3l__assembly_1__model_1 | I(q)

3h3l__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)