SAXSdb — 8duy

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

Cystathionine beta-lyase

Klebsiella pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0ZBA0_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–403； UniProt 1–395 Author chain B； PDBConstruct 9–403； UniProt 1–395 Author chain C； PDBConstruct 9–403； UniProt 1–395 Author chain D； PDBConstruct 9–403； UniProt 1–395

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	8duy
Deposition date deposition_date	2022-07-27
Structure title title	Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae
Keywords keywords	;SSGCID, Klebsiella pneumoniae, Cystathionine beta-lyase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, 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.

8duy__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8duy__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8duy__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.07 Å
Rg (electron density)	27.41 Å
Total Rg	27.97 Å
Atom count	6033
Residues	781
Excluded volume	107040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8duy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8duy__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 (4)

Entity 1 Entity 1 polymer

Description description	Cystathionine beta-lyase
Molecular weight formula_weight	44499.4 kDa
EC 编号 ec_number	4.4.1.8
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14023

MAHHHHHHMADKHLDTALVNAGRSKKYTQGSVNSVIQRASSLVFDTVEAKKHATRNRANGELFYGRRGTLTHFSLQEAMCELEGGAGCALFPCGAAAVANTILAFVEQGDHVLMTNTAYEPSQDFCTKILAKLGVTTSWFDPLIGADIARLVRPETRVVFLESPGSITMEVHDVPAIVAAVRQVAPEAIIMIDNTWAAGILFKALDFGIDISIQAGTKYLIGHSDAMVGTAVANARCWPQLRENAYLMGQMLDADTAYMTSRGLRTLGVRLRQHHESSLRIAEWLAQHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLSKRLNDAELAEYLDNFSLFSMAYSWGGFESLILANQPEQIAHIRPDAEVDFSGTLIRLHIGLENVDDLQADLAAGFARIV

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1682

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Unit-cell length a length_a	82.610 Å
Unit-cell length b length_b	131.140 Å
Unit-cell length c length_c	85.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	45.910 Å
R factor r_factor	0.1637
R_work r_work	0.1632
R_free r_free	0.1954

Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae

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

Cystathionine beta-lyase

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

8duy__assembly_2__model_1

8duy__assembly_2__model_1 | I(q)

8duy__assembly_2__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)

Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae

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

Cystathionine beta-lyase

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

8duy__assembly_2__model_1

8duy__assembly_2__model_1 | I(q)

8duy__assembly_2__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)