SAXSdb — 8stw

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

Cystathionine beta-synthase, K384N variant

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	PYRIDOXAL-5'-PHOSPHATE × 6 PROTOPORPHYRIN IX CONTAINING FE × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–363； UniProt 45–406 Author chain B； PDBConstruct 2–363； UniProt 45–406 Author chain C； PDBConstruct 2–363； UniProt 45–406 Author chain D； PDBConstruct 2–363； UniProt 45–406 Author chain E； PDBConstruct 2–363； UniProt 45–406 Author chain F； PDBConstruct 2–363； UniProt 45–406

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	8stw
Deposition date deposition_date	2023-05-11
Structure title title	K384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551)
Keywords keywords	PLP, Heme, hydrogen sulfide, LYASE; LYASE
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.

8stw__assembly_1__model_1

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

Download this curve (.dat)

8stw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8stw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.33 Å
Rg (electron density)	41.62 Å
Total Rg	41.99 Å
Atom count	16407
Residues	2118
Excluded volume	292410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8stw__assembly_1__model_1`	hexameric （6）	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	Cystathionine beta-synthase, K384N variant
Molecular weight formula_weight	39907.6 kDa
EC 编号 ec_number	4.2.1.22
Mutation mutation	K384N
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16481

MRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTNFLSDRWMLQKGFLKEEDLTEKK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	man
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

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Unit-cell length a length_a	89.462 Å
Unit-cell length b length_b	90.189 Å
Unit-cell length c length_c	104.224 Å
Unit-cell angle α angle_alpha	106.15 °
Unit-cell angle β angle_beta	105.49 °
Unit-cell angle γ angle_gamma	107.47 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	43.110 Å
R factor r_factor	0.2121
R_work r_work	0.2104
R_free r_free	0.2429

K384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551)

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

Cystathionine beta-synthase, K384N variant

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

8stw__assembly_1__model_1

8stw__assembly_1__model_1 | I(q)

8stw__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

7. Citations (1)

K384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551)

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

Cystathionine beta-synthase, K384N variant

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

8stw__assembly_1__model_1

8stw__assembly_1__model_1 | I(q)

8stw__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

7. Citations (1)