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9pc6

Antibody (1B2) Bound Crosslinked Rifamycin Synthetase Module 1 with a C-terminal Type II Thioesterase

Method: ELECTRON MICROSCOPY Dmax: 190.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

6-deoxyerythronolide-B synthase,RifR

Amycolatopsis mediterranei

UniProt O54666

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 631–2180 Chain B； UniProt 631–2180 Non-standard monomer：Yes (specific site not provided by mmCIF) Antibody Fragment 1B2 Heavy Chain × 2 Antibody Fragment 1B2 Light Chain × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH) cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.96 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 9PC6 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 experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2194–3157（964 aa）
Chain B 2194–3157（964 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
9PAT Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Transacylation Mode Deposited 2025-06-25 Different construct Different mutation/modification Different oligomeric state Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 631–2179（1549 aa）
Chain B 631–2179（1549 aa）
Chain C 631–2179（1549 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH)
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
9PAV Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode Deposited 2025-06-25 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 631–2179（1549 aa）
Chain B 631–2179（1549 aa）
Chain C 631–2179（1549 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH)
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O54666_AMYMD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 32–1581； UniProt 631–2180 Author chain B； PDBConstruct 32–1581； UniProt 631–2180

6-deoxyerythronolide-B synthase,RifR

Amycolatopsis mediterranei

UniProt Q7BUF9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 2–259 Chain B； UniProt 2–259 Non-standard monomer：Yes (specific site not provided by mmCIF) Antibody Fragment 1B2 Heavy Chain × 2 Antibody Fragment 1B2 Light Chain × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH) cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.96 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 9PC6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FLA RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 1 Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–259（259 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100 mM HEPES pH 7.0, 12% PEG 8000, 50 mM CaCl2, 2 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.202
3FLA RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 1 Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–259（259 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100 mM HEPES pH 7.0, 12% PEG 8000, 50 mM CaCl2, 2 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.202
3FLB RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 2 Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–259（259 aa）
Mutation：S94A CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100 mM HEPES pH 7.0, 12% PEG 8000, 50 mM CaCl2, 2 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.239

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q7BUF9_AMYMD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1592–1849； UniProt 2–259 Author chain B； PDBConstruct 1592–1849； UniProt 2–259

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 9pc6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9pc6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9pc6
Deposition date deposition_date2025-06-27
Structure title titleAntibody (1B2) Bound Crosslinked Rifamycin Synthetase Module 1 with a C-terminal Type II Thioesterase
Keywords keywordsPolyketide Synthase Module, Antibody (Fab), Transferase-Immune System complex; Transferase/Immune System
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier58.19 Å
Radius of gyration Rg (electron density) rg_electron58.03 Å
Forward intensity I(0) i02559450000.00
Molecular weight molecular_weight417480.0 kDa
Excluded volume excluded_volume520420 ų
Envelope volume envelope_volume807730 ų
Hydration-shell volume shell_volume117290 ų
Envelope diameter envelope_diameter192.3 Å
Shell Rg shell_rg59.09 Å
Envelope Rg envelope_rg56.33 Å
Shape Rg shape_rg58.03 Å
Total Rg total_rg58.08 Å
Total atoms total_atoms29408
Residues n_residues3975
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax190.5 Å
Rg (real space) rg_real58.02 Å
Rg uncertainty (real space) rg_real_error1.70 Å
I(0) (real space) i0_real2.5590e+09
I(0) uncertainty (real space) i0_real_error4.7180e+07
Rg (reciprocal space) rg_reciprocal58.30 Å
I(0) (reciprocal space) i0_reciprocal2560000000.0000
Solution quality estimate total_estimate0.8885
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.6 Å
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.581
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha124700000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.888
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)