← Back to search
6c9u

Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab)

Method: X-RAY DIFFRACTION Dmax: 159.1 Å Quality: GOOD
▼

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

6-deoxyerythronolide-B synthase EryA2, modules 3 and 4

Saccharopolyspora erythraea

UniProt Q03132

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 2–922 Fragment：[KS3][AT3] didomain from module 3 Non-standard monomer：Yes (specific site not provided by mmCIF) Light chain of Fab 1B2 × 2 Heavy chain of Fab 1B2 × 2 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

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 6C9U 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 oligomeric state 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
3EL6 Crystal Structure of the Erythromycin Dehydratase Deposited 2008-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2362–2653（292 aa） Fragment：EryDH4 (UNP residues 2362 to 2653)
Not recorded 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
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 3–923； UniProt 2–922

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6c9u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c9u
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6c9u
Deposition date deposition_date2018-01-28
Structure title titleCrystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab)
Keywords keywordsDEBS, PKS, polyketide synthase, 6-deoxyerthronolide B synthase, Fab, antibody, phage display, TRANSFERASE-immune system complex; TRANSFERASE/immune system
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier46.15 Å
Radius of gyration Rg (electron density) rg_electron46.55 Å
Forward intensity I(0) i0305176000.00
Molecular weight molecular_weight139450.0 kDa
Excluded volume excluded_volume173070 ų
Envelope volume envelope_volume249730 ų
Hydration-shell volume shell_volume48162 ų
Envelope diameter envelope_diameter167.7 Å
Shell Rg shell_rg45.98 Å
Envelope Rg envelope_rg46.04 Å
Shape Rg shape_rg46.54 Å
Total Rg total_rg46.56 Å
Total atoms total_atoms19444
Residues n_residues1310
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax159.1 Å
Rg (real space) rg_real46.59 Å
Rg uncertainty (real space) rg_real_error2.08 Å
I(0) (real space) i0_real3.0520e+08
I(0) uncertainty (real space) i0_real_error6.2280e+06
Rg (reciprocal space) rg_reciprocal46.16 Å
I(0) (reciprocal space) i0_reciprocal305000000.0000
Solution quality estimate total_estimate0.8120
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.4 Å
Skewness Skewness skewness0.461
Kurtosis Kurtosis kurtosis-0.370
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23880000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.832; Smooth: 0.410
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6c9ul1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6c9ul2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id6c9uH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c9uL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c9uL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

8. Citations (1)

▶

9. Files and Curves (10)