SAXSdb — 6gpe

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

Protein CsiD

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FE (II) ION × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	FE (II) ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSID_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–345； UniProt 1–325 Author chain B； PDBConstruct 21–345； UniProt 1–325

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	6gpe
Deposition date deposition_date	2018-06-05
Structure title title	Crystal Structure of the CsiD Glutarate Hydroxylase
Keywords keywords	jelly roll, glutarate hydroxylase, alpha-ketoglutarate-dependent, HYDROLASE; HYDROLASE
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.

6gpe__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6gpe__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6gpe__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	37.68 Å
Rg (electron density)	36.81 Å
Total Rg	37.44 Å
Atom count	9560
Residues	1168
Excluded volume	170000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6gpe__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6gpe__assembly_2__model_1`	tetrameric （4）	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	Protein CsiD
Molecular weight formula_weight	40646.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5325

MGSSHHHHHHSSGLVPRGSHMNALTAVQNNAVDSGQDYSGFTLTPSAQSPRLLELTFTEQTTKQFLEQVAEWPVQALEYKSFLRFRVAKILDDLCANQLQPLLLKTLLNRAEGALLINAVGVDDVKQADEMVKLATAVAHLIGRSNFDAMSGQYYARFVVKNVDNSDSYLRQPHRVMELHNDGTYVEEITDYVLMMKIDEQNMQGGNSLLLHLDDWEHLDNYFRHPLARRPMRFAAPPSKNVSKDVFHPVFDVDQQGRPVMRYIDQFVQPKDFEEGVWLSELSDAIETSKGILSVPVPVGKFLLINNLFWLHGRDRFTPHPDLRRELMRQRGYFAYASNHYQTHQLEHHHHHH

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6gpea_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.3 — Gab protein (hypothetical protein YgaT)

Domain ID domain_id	d6gpeb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.3 — Gab protein (hypothetical protein YgaT)

CATH v4.4 (2 domains)

Domain ID domain_id	6gpeA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

Domain ID domain_id	6gpeB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

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Unit-cell length a length_a	121.200 Å
Unit-cell length b length_b	121.200 Å
Unit-cell length c length_c	137.000 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 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	42.505 Å
R factor r_factor	0.1733
R_work r_work	0.1725
R_free r_free	0.1983

Crystal Structure of the CsiD Glutarate Hydroxylase

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

Protein CsiD

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

6gpe__assembly_2__model_1

6gpe__assembly_2__model_1 | I(q)

6gpe__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the CsiD Glutarate Hydroxylase

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

Protein CsiD

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

6gpe__assembly_2__model_1

6gpe__assembly_2__model_1 | I(q)

6gpe__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)