1cgk

CHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH NARINGENIN

Method: X-RAY DIFFRACTION Dmax: 79.1 Å Quality: GOOD

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

PROTEIN (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 1–389 Not recorded NAR NARINGENIN × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;THE DROPLE CONSISTED ON 25 MGR/ML (FINAL CONCENTRATION) PROTEIN MIXED WITH THE RESERVOIR WHICH CONTAINED 2.4 M AMMONIUM SULFATE, 100 MM PIPES BUFFER (PH 6.5) , IN THE PRESENCE (UP TO 5 MM) OR ABSENCE OF DTT REDUCING AGENT. CRYSTALS WERE STABILIZED IN 40% (V/V) PEG400, 100 MM PIPES 16 MM NARINGENIN PRIOR TO FREEZING AT 105 K, pH 6.50 Resolution 1.84 Å R-free 0.225

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 1–389; UniProt 1–389

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 1cgk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cgk
Deposition date deposition_date1999-03-25
Structure title titleCHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH NARINGENIN
Keywords keywordsPOLYKETIDE SYNTHASE, CHALCONE BIOSYNTHESIS, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.97
Radius of gyration Rg (electron density) rg_electron20.90
Forward intensity I(0) i029651300.00
Molecular weight molecular_weight42657.0 kDa
Excluded volume excluded_volume53797 ų
Envelope volume envelope_volume61427 ų
Hydration-shell volume shell_volume24125 ų
Envelope diameter envelope_diameter80.8
Shell Rg shell_rg28.19
Envelope Rg envelope_rg21.44
Shape Rg shape_rg20.90
Total Rg total_rg21.81
Total atoms total_atoms2994
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 dmax79.1
Rg (real space) rg_real21.91
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real2.9650e+07
I(0) uncertainty (real space) i0_real_error4.0970e+05
Rg (reciprocal space) rg_reciprocal21.92
I(0) (reciprocal space) i0_reciprocal29650000.0000
Solution quality estimate total_estimate0.8404
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.0
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.157
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6805000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.976

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1cgka1
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_idd1cgka2
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_id1cgkA01
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_id1cgkA02
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)