1d6h

CHALONE SYNTHASE (N336A MUTANT COMPLEXED WITH COA)

Method: X-RAY DIFFRACTION Dmax: 80.1 Å Quality: GOOD

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

CHALCONE SYNTHASE

Medicago sativa

UniProt P30074

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 3–389 Mutation:N336A Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 COA COENZYME A × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;2.2-2.4 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, 2 MM DITHIOTHREITOL (DTT), pH 6.5, VAPOR DIFFUSION, HANGING DROP Resolution 2.15 Å R-free 0.257

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.

15 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHS2_MEDSA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–387; UniProt 3–389

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 1d6h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d6h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d6h
Deposition date deposition_date1999-10-13
Structure title titleCHALONE SYNTHASE (N336A MUTANT COMPLEXED WITH COA)
Keywords keywordsPOLYPETIDE SYNTHASE, FLAVONOID BIOSYNTHESIS, MALONYL-COA DECARBOXYLATION, SITE-DIRECTED MUTANT, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.19
Radius of gyration Rg (electron density) rg_electron21.04
Forward intensity I(0) i031572000.00
Molecular weight molecular_weight43326.0 kDa
Excluded volume excluded_volume54316 ų
Envelope volume envelope_volume62519 ų
Hydration-shell volume shell_volume24402 ų
Envelope diameter envelope_diameter80.7
Shell Rg shell_rg28.31
Envelope Rg envelope_rg21.57
Shape Rg shape_rg21.03
Total Rg total_rg21.96
Total atoms total_atoms3032
Residues n_residues386
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax80.1
Rg (real space) rg_real22.14
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real3.1570e+07
I(0) uncertainty (real space) i0_real_error4.4280e+05
Rg (reciprocal space) rg_reciprocal22.15
I(0) (reciprocal space) i0_reciprocal31570000.0000
Solution quality estimate total_estimate0.8358
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.1
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.116
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7167000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.652; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.974

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d6ha1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like
Domain ID domain_idd1d6ha2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like

CATH v4.4 (2 domains)

Domain ID domain_id1d6hA01
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_id1d6hA02
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

8. Citations (1)

9. Files and Curves (10)