SAXSdb — 3fd0

▼

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

putative cystathionine beta-lyase involved in aluminum resistance

Listeria innocua

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 2 1,2-ETHANEDIOL × 56 DI(HYDROXYETHYL)ETHER × 6 TRIETHYLENE GLYCOL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q92C56_LISIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–409； UniProt 1–408 Author chain B； PDBConstruct 2–409； UniProt 1–408

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	3fd0
Deposition date deposition_date	2008-11-24
Structure title title	Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from LISTERIA INNOCUA at 2.12 A resolution
Keywords keywords	;NP_470671.1, putative cystathionine beta-lyase involved in aluminum resistance, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Unknown function, LYASE ;; LYASE
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.

3fd0__assembly_1__model_1

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

Download this curve (.dat)

3fd0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fd0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.25 Å
Rg (electron density)	34.60 Å
Total Rg	35.28 Å
Atom count	12866
Residues	1596
Excluded volume	230640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fd0__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	putative cystathionine beta-lyase involved in aluminum resistance
Molecular weight formula_weight	45315.8 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	6992

GMTEIQTIRKKVEQQITSLQNETDEIAEFNQAKVLDAFQENKVSDFHFNPSTGYGYDDEGRDTLERVYASVFKTEAALVRPQIISGTHAISTVLFGILRPGDELLYITGEPYDTLEEIVGIRSEGQGSLKDFQIGYDAVPLLPNGEIDYPAVSKKISANTKMIGIQRSRGYADRPSFTIEKIKEMVTFVKNINPNIIVFVDNCYGEFVERIEPTEVGADIIAGSLIKNPGGGLAKTGGYIAGRNTLVDLCGYRLTTPGIGREAGASLYSLLEMYQGFFLAPHVTAQAIKGARFTAAMLAEFGVEADPLWDAKRTDLIQSVSFHSKDKMIAFAQAIQAASPVNAHVLPIGAYMPGYEDDVIMAAGTFIQGASLELTADGPIREPYQLYVQGGLTYEHVKIAVTRAIENSL

Source Source

Source organism organism	Listeria innocua
NCBI taxonomy ID ncbi_taxonomy_id	1642
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	497

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3fd0A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	60 — Methioning gamme-lyase, C-terminal domain

Domain ID domain_id	3fd0A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	3fd0B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	60 — Methioning gamme-lyase, C-terminal domain

Domain ID domain_id	3fd0B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

▶

Unit-cell length a length_a	131.890 Å
Unit-cell length b length_b	131.890 Å
Unit-cell length c length_c	116.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.120 Å
Low-resolution limit resolution_low	29.185 Å
R factor r_factor	0.1540
R_work r_work	0.1520
R_free r_free	0.1880

Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from LISTERIA INNOCUA at 2.12 A resolution

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

putative cystathionine beta-lyase involved in aluminum resistance

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

3fd0__assembly_1__model_1

3fd0__assembly_1__model_1 | I(q)

3fd0__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from LISTERIA INNOCUA at 2.12 A resolution

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

putative cystathionine beta-lyase involved in aluminum resistance

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

3fd0__assembly_1__model_1

3fd0__assembly_1__model_1 | I(q)

3fd0__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)