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7s6b

Crystal structure of modular polyketide synthase apo-Lsd14 from the Lasalocid biosynthesis pathway, trapped in the transacylation step

Method: X-RAY DIFFRACTION Dmax: 173.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polyketide synthase

Streptomyces lasalocidi

UniProt B6ZK67

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–924 Chain B； UniProt 1–924 Chain C； UniProt 925–1468 Chain D； UniProt 925–1468 Chain E； UniProt 1469–1647 Fragment：KS and AT domains, residues 1-924 Fragment：KR domain, residues 925-1468 Fragment：ACP domain, residues 1469-1647 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；0.2 M lithium sulfate, 0.015 M magnesium sulfate, 0.1 M sodium acetate, pH 4.0, and 22% polyacrylic acid 5100 Resolution 2.35 Å R-free 0.241

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 7S6B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 38–1647（1610 aa）
Chain B 38–1647（1610 aa）
Chain C 38–1647（1610 aa）
Chain D 38–1647（1610 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 38–1647（1610 aa）
Chain B 38–1647（1610 aa）
Chain C 38–1647（1610 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

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

View Construct and Data Evidence
UniProt name B6ZK67_STRLS
Isoform —
PDB entities 1, 2, 3
Chains and sequence ranges Author chain A； PDBConstruct 21–944； UniProt 1–924 Author chain B； PDBConstruct 21–944； UniProt 1–924 Author chain C； PDBConstruct 1–544； UniProt 925–1468 Author chain D； PDBConstruct 1–544； UniProt 925–1468 Author chain E； PDBConstruct 1–179； UniProt 1469–1647

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 7s6b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7s6b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7s6b
Deposition date deposition_date2021-09-13
Structure title titleCrystal structure of modular polyketide synthase apo-Lsd14 from the Lasalocid biosynthesis pathway, trapped in the transacylation step
Keywords keywordsModular polyketide synthase, ketosynthase, acyltransferase, acyl carrier protein, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.16 Å
Radius of gyration Rg (electron density) rg_electron51.02 Å
Forward intensity I(0) i01382280000.00
Molecular weight molecular_weight300270.0 kDa
Excluded volume excluded_volume372380 ų
Envelope volume envelope_volume529640 ų
Hydration-shell volume shell_volume88967 ų
Envelope diameter envelope_diameter185.5 Å
Shell Rg shell_rg52.33 Å
Envelope Rg envelope_rg50.35 Å
Shape Rg shape_rg51.02 Å
Total Rg total_rg51.07 Å
Total atoms total_atoms41808
Residues n_residues2882
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 dmax173.4 Å
Rg (real space) rg_real51.14 Å
Rg uncertainty (real space) rg_real_error1.48 Å
I(0) (real space) i0_real1.3820e+09
I(0) uncertainty (real space) i0_real_error2.6300e+07
Rg (reciprocal space) rg_reciprocal51.17 Å
I(0) (reciprocal space) i0_reciprocal1382000000.0000
Solution quality estimate total_estimate0.8743
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary67.1 Å
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.240
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha100100000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.825
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7s6bA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id7s6bB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id7s6bE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily10 — ACP-like
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8. Citations (1)

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9. Files and Curves (10)