SAXSdb — 1cl2

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

CYSTATHIONINE BETA-LYASE

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395	Not recorded	PPG (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.2；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2)	Resolution 2.20 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1CL2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CL1 CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI Deposited 1997-09-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） Chain B 1–395（395 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	BCT BICARBONATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2)	Resolution 1.83 Å R-free 0.221
2FQ6 Cystathionine beta-lyase (cbl) from escherichia coli in complex with n-hydrazinocarbonylmethyl-2-trifluoromethyl-benzamide Deposited 2006-01-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） Chain B 1–395（395 aa）	Not recorded	P3F PHOSPHORIC ACID MONO-(5-HYDROXY-6-METHYL-4-{[2-(2-TRIFLUOROMETHYL-BENZOYLAMINO)-ACETYL]-HYDRAZONOMETHYL}-PYRIDIN-3-YLMETHYL)ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.1M Hepes, 0.15M calcium chloride, 26% PEG 400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.78 Å R-free 0.225
2GQN Cystathionine Beta-Lyase (CBL) from Escherichia Coli in complex with N-Hydrazinocarbonylmethyl-2-Nitro-Benzamide Deposited 2006-04-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） Chain B 1–395（395 aa）	Not recorded	BLP (5-HYDROXY-6-METHYL-4-((2-(2-(2-NITROBENZAMIDO)ACETYL)HYDRAZINYL)METHYL)PYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.1M Hepes, 0.15M calcium chloride, and 26% PEG400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.227
4ITG P113S mutant of E. coli Cystathionine beta-lyase MetC Deposited 2013-01-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） Chain B 1–395（395 aa）	Mutation：P113S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：P113S Non-standard monomer：Yes (specific site not provided by mmCIF)	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.74 Å R-free 0.198
4ITX P113S mutant of E. coli Cystathionine beta-lyase MetC inhibited by reaction with L-Ala-P Deposited 2013-01-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） Chain B 1–395（395 aa）	Mutation：P113S Mutation：P113S	IN5 {1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.61 Å R-free 0.195

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	METC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 1–395； 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	1cl2
Deposition date deposition_date	1997-09-04
Structure title title	CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINE
Keywords keywords	METHIONINE BIOSYNTHESIS, PLP-DEPENDENT ENZYMES, C-S BETA LYASE, AMINOETHOXYVINYLGLYCINE, SLOW-BINDING INHIBITION; METHIONINE BIOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.83 Å
Radius of gyration Rg (electron density) rg_electron	33.51 Å
Forward intensity I(0) i0	112115000.00
Molecular weight molecular_weight	85346.0 kDa
Excluded volume excluded_volume	106870 Å³
Envelope volume envelope_volume	135860 Å³
Hydration-shell volume shell_volume	33454 Å³
Envelope diameter envelope_diameter	110.6 Å
Shell Rg shell_rg	41.13 Å
Envelope Rg envelope_rg	32.68 Å
Shape Rg shape_rg	33.54 Å
Total Rg total_rg	33.96 Å
Total atoms total_atoms	7325
Residues n_residues	783
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.5 Å
Rg (real space) rg_real	33.87 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.1210e+08
I(0) uncertainty (real space) i0_real_error	1.7490e+06
Rg (reciprocal space) rg_reciprocal	33.85 Å
I(0) (reciprocal space) i0_reciprocal	112100000.0000
Solution quality estimate total_estimate	0.8804
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.228
Kurtosis Kurtosis kurtosis	-0.823
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35610000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.906

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CYSTATHIONINE BETA-LYASE
Molecular weight formula_weight	43261.3 kDa
EC 编号 ec_number	4.4.1.8
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	8615

MADKKLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARIV

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid
Molecular weight formula_weight	389.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	430

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cl2a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1cl2b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1cl2A01
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	1cl2A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1cl2B01
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	1cl2B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

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8. Citations (2)

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Unit-cell length a length_a	61.100 Å
Unit-cell length b length_b	154.700 Å
Unit-cell length c length_c	152.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1640
R_work r_work	0.1640
R_free r_free	—

fit	/app/data/saxs_computation/cl/1cl2/1cl2.fit
pddf	/app/data/pr_computation/cl/1cl2/1cl2.pr.out
profile	/app/data/saxs_computation/cl/1cl2/1cl2.dat

CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINE

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction