1jdi

CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE

Method: X-RAY DIFFRACTION

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

L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE

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	ZINC ION × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 water × 4	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARAD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–231； UniProt 1–231 Author chain B； PDBConstruct 1–231； UniProt 1–231 Author chain C； PDBConstruct 1–231； UniProt 1–231 Author chain D； PDBConstruct 1–231； UniProt 1–231 Author chain E； PDBConstruct 1–231； UniProt 1–231 Author chain F； PDBConstruct 1–231； UniProt 1–231

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	1jdi
Deposition date deposition_date	2001-06-13
Structure title title	CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE
Keywords keywords	epimerase, ribulose, aldolase, ISOMERASE; 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.

1jdi__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1jdi__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jdi__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	29.73 Å
Rg (electron density)	28.74 Å
Total Rg	29.54 Å
Atom count	6944
Residues	892
Excluded volume	123130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jdi__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jdi__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1jdi__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1jdi__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1jdi__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1jdi__assembly_6__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1jdi__assembly_7__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	L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
Molecular weight formula_weight	25531.9 kDa
EC 编号 ec_number	5.1.3.4
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	10849

MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPSGVDYSIMTADDMVVVSIETGEVVEGAKKPSSDTPTHRLLYQAFPSIGGIVHTHSRHATIWAQAGQSIPATGTTHADYFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQGIDAAQMPGVLVHSHGPFAWGKNAEDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLNKHYLRKHGAKAYYGQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	433

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1jdia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.1 — AraD-like aldolase/epimerase

Domain ID domain_id	d1jdib_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.1 — AraD-like aldolase/epimerase

Domain ID domain_id	d1jdic_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.1 — AraD-like aldolase/epimerase

Domain ID domain_id	d1jdid_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.1 — AraD-like aldolase/epimerase

Domain ID domain_id	d1jdie_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.1 — AraD-like aldolase/epimerase

Domain ID domain_id	d1jdif_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.1 — AraD-like aldolase/epimerase

CATH v4.4 (6 domains)

Domain ID domain_id	1jdiA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	1jdiB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	1jdiC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	1jdiD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	1jdiE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	1jdiF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

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Unit-cell length a length_a	105.900 Å
Unit-cell length b length_b	105.900 Å
Unit-cell length c length_c	274.800 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	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2410

CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE

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

L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE

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

1jdi__assembly_4__model_1

1jdi__assembly_4__model_1 | I(q)

1jdi__assembly_4__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE

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

L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE

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

1jdi__assembly_4__model_1

1jdi__assembly_4__model_1 | I(q)

1jdi__assembly_4__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)