SAXSdb — 1j2r

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

Hypothetical isochorismatase family protein yecD

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	(4S)-2-METHYL-2,4-PENTANEDIOL × 12 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	(4S)-2-METHYL-2,4-PENTANEDIOL × 6 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	(4S)-2-METHYL-2,4-PENTANEDIOL × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YECD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–199； UniProt 1–199 Author chain B； PDBConstruct 1–199； UniProt 1–199 Author chain C； PDBConstruct 1–199； UniProt 1–199 Author chain D； PDBConstruct 1–199； UniProt 1–199

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	1j2r
Deposition date deposition_date	2003-01-09
Structure title title	Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution
Keywords keywords	;parallel beta-sheet 3-2-1-4-5-6, alpha-beta-alpha motif, tetramere, structural genomics, Bacterial targets at IGS-CNRS, France, BIGS, unknown function ;; Structural genomics, unknown function
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.

1j2r__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1j2r__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1j2r__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	21.75 Å
Rg (electron density)	20.63 Å
Total Rg	21.55 Å
Atom count	2932
Residues	375
Excluded volume	52278 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1j2r__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1j2r__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1j2r__assembly_3__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical isochorismatase family protein yecD
Molecular weight formula_weight	21794.7 kDa
Mutation mutation	A103T
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6771

MRHDFVFSGVIMLELNAKTTALVVIDLQEGILPFAGGPHTADEVVNRAGKLAAKFRASGQPVFLVRVGWSADYAEALKQPVDAPSPAKVLPENWWQHPAALGTTDSDIEIIKRQWGAFYGTDLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFNLVIAEDACSAASAEQHNNSINHIYPRIARVRSVEEILNAL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	924

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1j2ra_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.33 — Isochorismatase-like hydrolases
Superfamily Superfamily superfamily	c.33.1 — Isochorismatase-like hydrolases
Family Family family	c.33.1.3 — Isochorismatase-like hydrolases

Domain ID domain_id	d1j2rb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.33 — Isochorismatase-like hydrolases
Superfamily Superfamily superfamily	c.33.1 — Isochorismatase-like hydrolases
Family Family family	c.33.1.3 — Isochorismatase-like hydrolases

Domain ID domain_id	d1j2rc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.33 — Isochorismatase-like hydrolases
Superfamily Superfamily superfamily	c.33.1 — Isochorismatase-like hydrolases
Family Family family	c.33.1.3 — Isochorismatase-like hydrolases

Domain ID domain_id	d1j2rd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.33 — Isochorismatase-like hydrolases
Superfamily Superfamily superfamily	c.33.1 — Isochorismatase-like hydrolases
Family Family family	c.33.1.3 — Isochorismatase-like hydrolases

CATH v4.4 (4 domains)

Domain ID domain_id	1j2rA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	850 — Isochorismatase-like

Domain ID domain_id	1j2rB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	850 — Isochorismatase-like

Domain ID domain_id	1j2rC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	850 — Isochorismatase-like

Domain ID domain_id	1j2rD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	850 — Isochorismatase-like

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Unit-cell length a length_a	140.502 Å
Unit-cell length b length_b	108.886 Å
Unit-cell length c length_c	50.419 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	50.770 Å
R factor r_factor	0.1460
R_work r_work	0.1450
R_free r_free	0.1649

Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution

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

Hypothetical isochorismatase family protein yecD

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

1j2r__assembly_3__model_1

1j2r__assembly_3__model_1 | I(q)

1j2r__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution

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

Hypothetical isochorismatase family protein yecD

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

1j2r__assembly_3__model_1

1j2r__assembly_3__model_1 | I(q)

1j2r__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)