SAXSdb — 1f89

▼

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

32.5 KDA PROTEIN YLR351C

Saccharomyces cerevisiae

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIT3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–291； UniProt 1–291 Author chain B； PDBConstruct 1–291； UniProt 1–291

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1f89
Deposition date deposition_date	2000-06-29
Structure title title	Crystal structure of Saccharomyces cerevisiae Nit3, a member of branch 10 of the nitrilase superfamily
Keywords keywords	;Nitrilase, Dimer, Structural Genomics, Four layer sandwich, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1f89__assembly_1__model_1

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

Download this curve (.dat)

1f89__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1f89__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.56 Å
Rg (electron density)	25.86 Å
Total Rg	26.70 Å
Atom count	4274
Residues	542
Excluded volume	76560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1f89__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1f89a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.160 — Carbon-nitrogen hydrolase
Superfamily Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
Family Family family	d.160.1.1 — Nitrilase

Domain ID domain_id	d1f89b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.160 — Carbon-nitrogen hydrolase
Superfamily Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
Family Family family	d.160.1.1 — Nitrilase

CATH v4.4 (2 domains)

Domain ID domain_id	1f89A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	1f89B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

▶

Unit-cell length a length_a	73.523 Å
Unit-cell length b length_b	53.492 Å
Unit-cell length c length_c	80.985 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.43 °
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	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.2580

Description description	32.5 KDA PROTEIN YLR351C
Molecular weight formula_weight	32591.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4391

Crystal structure of Saccharomyces cerevisiae Nit3, a member of branch 10 of the nitrilase superfamily

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

32.5 KDA PROTEIN YLR351C

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

1f89__assembly_1__model_1

1f89__assembly_1__model_1 | I(q)

1f89__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

Crystal structure of Saccharomyces cerevisiae Nit3, a member of branch 10 of the nitrilase superfamily

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

32.5 KDA PROTEIN YLR351C

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

1f89__assembly_1__model_1

1f89__assembly_1__model_1 | I(q)

1f89__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)