1d6i

CHALCONE SYNTHASE (H303Q MUTANT)

Method: X-RAY DIFFRACTION Dmax: 121.4 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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–389 Chain B; UniProt 2–389 Fragment:CHS Mutation:H303Q Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 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 2.00 Å R-free 0.269
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–389 Chain B; UniProt 2–389 Fragment:CHS Mutation:H303Q Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 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 2.00 Å R-free 0.269

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 16 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 1–388; UniProt 2–389 Author chain B; PDBConstruct 1–388; UniProt 2–389

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 1d6i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d6i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d6i
Deposition date deposition_date1999-10-13
Structure title titleCHALCONE SYNTHASE (H303Q MUTANT)
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_guinier36.23
Radius of gyration Rg (electron density) rg_electron35.93
Forward intensity I(0) i0108675000.00
Molecular weight molecular_weight85154.0 kDa
Excluded volume excluded_volume107270 ų
Envelope volume envelope_volume136080 ų
Hydration-shell volume shell_volume33185 ų
Envelope diameter envelope_diameter121.3
Shell Rg shell_rg39.77
Envelope Rg envelope_rg35.71
Shape Rg shape_rg35.92
Total Rg total_rg36.25
Total atoms total_atoms5970
Residues n_residues772
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 dmax121.4
Rg (real space) rg_real36.52
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real1.0870e+08
I(0) uncertainty (real space) i0_real_error1.8630e+06
Rg (reciprocal space) rg_reciprocal36.34
I(0) (reciprocal space) i0_reciprocal108700000.0000
Solution quality estimate total_estimate0.8037
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.6
Skewness Skewness skewness0.397
Kurtosis Kurtosis kurtosis-0.743
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25220000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.667; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.596; Smooth: 0.846

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1d6ia1
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_idd1d6ia2
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_idd1d6ib1
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_idd1d6ib2
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 (4 domains)

Domain ID domain_id1d6iA01
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_id1d6iA02
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_id1d6iB01
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_id1d6iB02
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)