SAXSdb — 3el6

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

Erythromycin dehydratase

Saccharopolyspora erythraea

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2362–2653	Fragment：EryDH4 (UNP residues 2362 to 2653)	SO4 SULFATE ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；2.15 M ammonium sulfate, 100 mM sodium cacodylate pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.227

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 3EL6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11SZ Antibody (1B2) Bound Rifamycin Synthetase Module 2 Deposited 2026-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 3489–3567（79 aa） Chain B 3489–3567（79 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
1PZQ Structure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS 2 and DEBS 3: The A domain Deposited 2003-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3490–3547（58 aa） Fragment：C-terminal fragment Chain B 3490–3547（58 aa） Fragment：C-terminal fragment	Mutation：L1G, F2S Mutation：L1G, F2S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer NA；Pressure ambient NMR sample composition 1mM DOCK23 U-15N,13C: 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM DOCK23 (50% U-15N,13C: 50% unlabeled): 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1PZR Structure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS2 and DEBS3: the B domain Deposited 2003-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3548–3567（20 aa） Fragment：RESIDUES 61-120 Chain B 3548–3567（20 aa） Fragment：RESIDUES 61-120	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer NA；Pressure ambient NMR sample composition 1mM DOCK23 U-15N,13C: 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM DOCK23 (50% U-15N,13C: 50% unlabeled): 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
6C9U Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab) Deposited 2018-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–922（921 aa） Fragment：[KS3][AT3] didomain from module 3	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；200 mM potassium citrate, 20%(w/v) PEG 3,350 and 12% ethylene glycol)	Resolution 2.09 Å R-free 0.210
7M7E 6-Deoxyerythronolide B synthase (DEBS) hybrid module (M3/1) in complex with antibody fragment 1B2 Deposited 2021-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–922（921 aa） Fragment：EryA2 (UNP residues 2-922) + EryA1 (UNP residues 1457-2015) + EryA3 (UNP residues 2896-3172) Chain B 2–922（921 aa） Fragment：EryA2 (UNP residues 2-922) + EryA1 (UNP residues 1457-2015) + EryA3 (UNP residues 2896-3172)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7S6C CryoEM structure of modular PKS holo-Lsd14 stalled at the condensation step and bound to antibody fragment 1B2, composite structure Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 2–30（29 aa） Chain B 2–30（29 aa） Chain C 2–30（29 aa） Chain D 2–30（29 aa）	Not recorded	ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 5 seconds before plunging in liquid ethane.	Resolution 3.10 Å
7S6D CryoEM structure of modular PKS holo-Lsd14 bound to antibody fragment 1B2, composite structure Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 2–30（29 aa） Chain B 2–30（29 aa） Chain C 2–30（29 aa）	Not recorded	ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 5 seconds before plunging in liquid ethane.	Resolution 3.10 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ERYA2_SACER
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–313； UniProt 2362–2653

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	3el6
Deposition date deposition_date	2008-09-20
Structure title title	Crystal Structure of the Erythromycin Dehydratase
Keywords keywords	;Dehydratase Double hotdog fold Cis-proline, Acyltransferase, Antibiotic biosynthesis, Multifunctional enzyme, NADP, Phosphopantetheine, Transferase, LYASE ;; LYASE
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	20.04 Å
Radius of gyration Rg (electron density) rg_electron	18.57 Å
Forward intensity I(0) i0	14802200.00
Molecular weight molecular_weight	28266.0 kDa
Excluded volume excluded_volume	35141 Å³
Envelope volume envelope_volume	41797 Å³
Hydration-shell volume shell_volume	18998 Å³
Envelope diameter envelope_diameter	67.6 Å
Shell Rg shell_rg	24.78 Å
Envelope Rg envelope_rg	18.90 Å
Shape Rg shape_rg	18.56 Å
Total Rg total_rg	19.51 Å
Total atoms total_atoms	1995
Residues n_residues	271
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	65.0 Å
Rg (real space) rg_real	19.97 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.4800e+07
I(0) uncertainty (real space) i0_real_error	1.8300e+05
Rg (reciprocal space) rg_reciprocal	19.98 Å
I(0) (reciprocal space) i0_reciprocal	14800000.0000
Solution quality estimate total_estimate	0.8062
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.270
Kurtosis Kurtosis kurtosis	-0.246
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3013000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Erythromycin dehydratase
Molecular weight formula_weight	32717.4 kDa
EC 编号 ec_number	4.2.1.61
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2242

MGSSHHHHHHSSGLVPRGSHMHRPADVSALGVRGAEHPLLLAAVDVPGHGGAVFTGRLSTDEQPWLAEHVVGGRTLVPGSVLVDLALAAGEDVGLPVLEELVLQRPLVLAGAGALLRMSVGAPDESGRRTIDVHAAEDVADLADAQWSQHATGTLAQGVAAGPRDTEQWPPEDAVRIPLDDHYDGLAEQGYEYGPSFQALRAAWRKDDSVYAEVSIAADEEGYAFHPVLLDAVAQTLSLGALGEPGGGKLPFAWNTVTLHASGATSVRVVATPAGADAMALRVTDPAGHLVATVDSLVVRSTGEKWEQPEPRG

来源 Source

来源生物 organism	Saccharopolyspora erythraea
NCBI Class编号 ncbi_taxonomy_id	1836
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3el6A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	110 — Polyketide synthase dehydratase

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8. Citations (1)

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Unit-cell length a length_a	66.997 Å
Unit-cell length b length_b	66.997 Å
Unit-cell length c length_c	186.238 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	45.550 Å
R factor r_factor	0.2003
R_work r_work	0.1972
R_free r_free	0.2269

fit	/app/data/saxs_computation/el/3el6/3el6.fit
pddf	/app/data/pr_computation/el/3el6/3el6.pr.out
profile	/app/data/saxs_computation/el/3el6/3el6.dat

Crystal Structure of the Erythromycin Dehydratase

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

Erythromycin dehydratase

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