SAXSdb — 3i24

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

HIT family hydrolase

Vibrio fischeri ES114

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 19 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5E3V1_VIBF1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–141； UniProt 1–141 Author chain B； PDBConstruct 1–141； UniProt 1–141

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	3i24
Deposition date deposition_date	2009-06-29
Structure title title	Crystal Structure of a HIT family hydrolase protein from Vibrio fischeri. Northeast Structural Genomics Consortium target id VfR176
Keywords keywords	;HIT family hydrolase, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

3i24__assembly_1__model_1

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

Download this curve (.dat)

3i24__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3i24__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.95 Å
Rg (electron density)	18.49 Å
Total Rg	19.46 Å
Atom count	2259
Residues	282
Excluded volume	41126 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3i24__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 (3)

Entity 1 Entity 1 polymer

Description description	HIT family hydrolase
Molecular weight formula_weight	17020.6 kDa
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	2679

MAFQLHPRLQQDCIVLGNLPLCKVLLIKEDIGPWLILVPRIEELKEIHHMTDEQQIQFIKESSAVAQLLEDNFSPDKINIGALGNLVPQLHIHHIARFTTDVAWPGPVWGNTTGVIRAQSSQTQLVDLLRDKLSNISGFKRLEHHHHHH

Source Source

Source organism organism	Vibrio fischeri ES114
NCBI taxonomy ID ncbi_taxonomy_id	312309
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	420

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3i24A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

Domain ID domain_id	3i24B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

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Unit-cell length a length_a	43.433 Å
Unit-cell length b length_b	69.312 Å
Unit-cell length c length_c	49.077 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	27.740 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2150

Crystal Structure of a HIT family hydrolase protein from Vibrio fischeri. Northeast Structural Genomics Consortium target id VfR176

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

HIT family 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

3i24__assembly_1__model_1

3i24__assembly_1__model_1 | I(q)

3i24__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of a HIT family hydrolase protein from Vibrio fischeri. Northeast Structural Genomics Consortium target id VfR176

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

HIT family 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

3i24__assembly_1__model_1

3i24__assembly_1__model_1 | I(q)

3i24__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)