SAXSdb — 4d06

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

CHALCONE ISOMERASE

EUBACTERIUM RAMULUS

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–283 Chain B； UniProt 1–283 Chain C； UniProt 1–283 Chain D； UniProt 1–283 Chain E； UniProt 1–283 Chain F； UniProt 1–283	Not recorded	NAR NARINGENIN × 7 CL CHLORIDE ION × 17 X8W (2E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.1 M HEPES PH 7.5, 0.2 M SODIUM CHLORIDE, 1.6 M AMMONIUM SULFATE, 380 MIKROM NARINGENIN CHALCONE DISSOLVED IN ETHANOL	Resolution 2.00 Å R-free 0.163

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 4D06	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4D4F Mutant P250A of bacterial chalcone isomerase from Eubacterium ramulus Deposited 2014-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–283（283 aa） Chain B 1–283（283 aa） Chain C 1–283（283 aa） Chain D 1–283（283 aa） Chain E 1–283（283 aa） Chain F 1–283（283 aa）	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	GOL GLYCEROL × 11 CL CHLORIDE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2.0 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.5, 0.2 SODIUM CHLORIDE; CRYO: 2.4 M AMMONIUM SULPHATE, 22% GLYCEROL, 0.1 M HEPES PH 7.5, 0.2 SODIUM CHLORIDE	Resolution 2.34 Å R-free 0.175
8B7R Bacterial chalcone isomerase with taxifolin chalcone Deposited 2022-10-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–283（283 aa） Chain B 1–283（283 aa） Chain C 1–283（283 aa） Chain D 1–283（283 aa） Chain E 1–283（283 aa） Chain F 1–283（283 aa）	Not recorded	Q0X (Z)-3-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-1-[2,4,6-tris(oxidanyl)phenyl]prop-2-en-1-one × 6 CL CHLORIDE ION × 26 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.8 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)	Resolution 2.15 Å R-free 0.190
8B7U Bacterial chalcone isomerase H33A with taxifolin Deposited 2022-10-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–283（283 aa） Chain B 1–283（283 aa） Chain K 1–283（283 aa） Chain L 1–283（283 aa） Chain M 1–283（283 aa） Chain N 1–283（283 aa）	Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A	DQH (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE × 12 CL CHLORIDE ION × 18 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Hanging drop 2+2 ul. soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)	Resolution 2.80 Å R-free 0.225
8B7U Bacterial chalcone isomerase H33A with taxifolin Deposited 2022-10-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 1–283（283 aa） Chain D 1–283（283 aa） Chain E 1–283（283 aa） Chain F 1–283（283 aa） Chain G 1–283（283 aa） Chain H 1–283（283 aa）	Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A	DQH (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE × 12 CL CHLORIDE ION × 16 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 K POTASSIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Hanging drop 2+2 ul. soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)	Resolution 2.80 Å R-free 0.225
8B7U Bacterial chalcone isomerase H33A with taxifolin Deposited 2022-10-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain I 1–283（283 aa） Chain J 1–283（283 aa） Chain O 1–283（283 aa） Chain P 1–283（283 aa） Chain Q 1–283（283 aa） Chain R 1–283（283 aa）	Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A	DQH (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE × 11 CL CHLORIDE ION × 13 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Hanging drop 2+2 ul. soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)	Resolution 2.80 Å R-free 0.225
8B7Z Bacterial chalcone isomerase H33A with taxifolin Deposited 2022-10-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–283（283 aa） Chain B 1–283（283 aa） Chain K 1–283（283 aa） Chain L 1–283（283 aa） Chain M 1–283（283 aa） Chain N 1–283（283 aa）	Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A	DQH (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE × 16 GOL GLYCEROL × 1 SO4 SULFATE ION × 3 K POTASSIUM ION × 1 CL CHLORIDE ION × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)	Resolution 3.00 Å R-free 0.268
8B7Z Bacterial chalcone isomerase H33A with taxifolin Deposited 2022-10-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 1–283（283 aa） Chain D 1–283（283 aa） Chain E 1–283（283 aa） Chain F 1–283（283 aa） Chain G 1–283（283 aa） Chain H 1–283（283 aa）	Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A	DQH (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE × 12 SO4 SULFATE ION × 3 K POTASSIUM ION × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)	Resolution 3.00 Å R-free 0.268
8B7Z Bacterial chalcone isomerase H33A with taxifolin Deposited 2022-10-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain I 1–283（283 aa） Chain J 1–283（283 aa） Chain O 1–283（283 aa） Chain P 1–283（283 aa） Chain Q 1–283（283 aa） Chain R 1–283（283 aa）	Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A Mutation：H33A	DQH (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE × 17 SO4 SULFATE ION × 2 CL CHLORIDE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)	Resolution 3.00 Å R-free 0.268

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	V9P0A9_9FIRM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 1–283 Author chain B； PDBConstruct 1–283； UniProt 1–283 Author chain C； PDBConstruct 1–283； UniProt 1–283 Author chain D； PDBConstruct 1–283； UniProt 1–283 Author chain E； PDBConstruct 1–283； UniProt 1–283 Author chain F； PDBConstruct 1–283； UniProt 1–283

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4d06
Deposition date deposition_date	2014-04-24
Structure title title	Bacterial chalcone isomerase complexed with naringenin
Keywords keywords	ISOMERASE, BACTERIAL CHALCONE ISOMERASE, FLAVONOIDS, NARINGENIN; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	34.82 Å
Radius of gyration Rg (electron density) rg_electron	33.95 Å
Forward intensity I(0) i0	520346000.00
Molecular weight molecular_weight	190430.0 kDa
Excluded volume excluded_volume	239660 Å³
Envelope volume envelope_volume	280430 Å³
Hydration-shell volume shell_volume	64638 Å³
Envelope diameter envelope_diameter	113.4 Å
Shell Rg shell_rg	43.15 Å
Envelope Rg envelope_rg	34.10 Å
Shape Rg shape_rg	33.91 Å
Total Rg total_rg	34.69 Å
Total atoms total_atoms	13439
Residues n_residues	1623
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.3 Å
Rg (real space) rg_real	34.59 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	5.2030e+08
I(0) uncertainty (real space) i0_real_error	7.1220e+06
Rg (reciprocal space) rg_reciprocal	34.73 Å
I(0) (reciprocal space) i0_reciprocal	520400000.0000
Solution quality estimate total_estimate	0.6784
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.2 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.497
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	312300000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.966; Smooth: 0.915

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	CHALCONE ISOMERASE
Molecular weight formula_weight	32537.9 kDa
EC 编号 ec_number	5.5.1.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15609

MADFKFEPMRSLIYVDCVSEDYRPKLQRWIYKVHIPDSISQFEPYVTKYAFYPSFPIPPQGDRFGYARMQLTEHHWLVSDLDPRLEIKAIAETFPMDVLVWQGQIPAAAHTDAQIDSDGDAGNAARKSNNAEGNPFIFAFLPMWWEKDLKGKGRTIEDGANYRFNMTIGFPEGVDKAEGEKWLFEKVVPILQAAPECTRVLASAVKKDINGCVMDWVLEIWFENQSGWYKVMVDDMKALEKPSWAQQDAFPFLKPYHNVCSAAVADYTPSNNLANYRGYITMR

来源 Source

来源生物 organism	EUBACTERIUM RAMULUS
NCBI Class编号 ncbi_taxonomy_id	39490
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	NARINGENIN
Molecular weight formula_weight	272.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 non-polymer

Description description	(2E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
Molecular weight formula_weight	272.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1895

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8. Citations (1)

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Unit-cell length a length_a	181.165 Å
Unit-cell length b length_b	187.991 Å
Unit-cell length c length_c	196.221 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	49.180 Å
R factor r_factor	0.1414
R_work r_work	0.1402
R_free r_free	0.1628

fit	/app/data/saxs_computation/d0/4d06/4d06.fit
pddf	/app/data/pr_computation/d0/4d06/4d06.pr.out
profile	/app/data/saxs_computation/d0/4d06/4d06.dat

Bacterial chalcone isomerase complexed with naringenin

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

CHALCONE ISOMERASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction