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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	NARINGENIN × 7 CHLORIDE ION × 17 (2E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one × 2 GLYCEROL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4d06__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4d06__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4d06__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.82 Å
Rg (electron density)	33.95 Å
Total Rg	34.69 Å
Atom count	13439
Residues	1623
Excluded volume	239660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4d06__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	EUBACTERIUM RAMULUS
NCBI taxonomy ID ncbi_taxonomy_id	39490
Host organism 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4d06__assembly_1__model_1

4d06__assembly_1__model_1 | I(q)

4d06__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4d06__assembly_1__model_1

4d06__assembly_1__model_1 | I(q)

4d06__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)