SAXSdb — 1xbx

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

3-keto-L-gulonate 6-phosphate decarboxylase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5-O-phosphono-L-ribulose × 1 MAGNESIUM ION × 2 RIBULOSE-5-PHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	5-O-phosphono-L-ribulose × 2 MAGNESIUM ION × 4 RIBULOSE-5-PHOSPHATE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ULAD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 1–216 Author chain B； PDBConstruct 1–216； UniProt 1–216

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	1xbx
Deposition date deposition_date	2004-08-31
Structure title title	Structure of 3-keto-L-gulonate 6-phosphate decarboxylase E112D/R139V/T169A mutant with bound D-ribulose 5-phosphate
Keywords keywords	TIM barrel, UNKNOWN FUNCTION; 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.

1xbx__assembly_1__model_1

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

Download this curve (.dat)

1xbx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xbx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.23 Å
Rg (electron density)	21.48 Å
Total Rg	22.25 Å
Atom count	3283
Residues	428
Excluded volume	58626 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xbx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xbx__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 (5)

Entity 1 Entity 1 polymer

Description description	3-keto-L-gulonate 6-phosphate decarboxylase
Molecular weight formula_weight	23500.9 kDa
Mutation mutation	E112D/R139V/T169A
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	3777

MSLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIDLTGYWTWEQAQQWRDAGIGQVVYHRSVDAQAAGVAWGEADITAIKRLSDMGFKVTVAGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELWG

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	5-O-phosphono-L-ribulose
Molecular weight formula_weight	230.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	RIBULOSE-5-PHOSPHATE
Molecular weight formula_weight	230.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	494

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xbxa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.3 — Decarboxylase

Domain ID domain_id	d1xbxb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.3 — Decarboxylase

CATH v4.4 (2 domains)

Domain ID domain_id	1xbxA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1xbxB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	123.000 Å
Unit-cell length b length_b	41.831 Å
Unit-cell length c length_c	91.068 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	90.000 Å
R factor r_factor	0.1425
R_work r_work	0.1406
R_free r_free	0.1776

Structure of 3-keto-L-gulonate 6-phosphate decarboxylase E112D/R139V/T169A mutant with bound D-ribulose 5-phosphate

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

3-keto-L-gulonate 6-phosphate decarboxylase

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

1xbx__assembly_1__model_1

1xbx__assembly_1__model_1 | I(q)

1xbx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of 3-keto-L-gulonate 6-phosphate decarboxylase E112D/R139V/T169A mutant with bound D-ribulose 5-phosphate

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

3-keto-L-gulonate 6-phosphate decarboxylase

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

1xbx__assembly_1__model_1

1xbx__assembly_1__model_1 | I(q)

1xbx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)