SAXSdb — 1oj4

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

4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPE_ECOL6
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

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	1oj4
Deposition date deposition_date	2003-06-30
Structure title title	Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Keywords keywords	TRANSFERASE, KINASE, ISOPRENOIDS BIOSYNTHESIS, GHMP KINASE SUPERFAMILY TRANSFERASE; TRANSFERASE
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.

1oj4__assembly_1__model_1

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

Download this curve (.dat)

1oj4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1oj4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.11 Å
Rg (electron density)	19.08 Å
Total Rg	19.96 Å
Atom count	2243
Residues	277
Excluded volume	39828 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1oj4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1oj4__assembly_2__model_1`	monomeric （1）	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	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
Molecular weight formula_weight	31266.7 kDa
EC 编号 ec_number	2.7.1.148
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	5011

MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAML

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	217992
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
Molecular weight formula_weight	521.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
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	383

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1oj4a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.5 — GHMP Kinase, N-terminal domain

Domain ID domain_id	d1oj4a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.26 — GHMP Kinase, C-terminal domain
Family Family family	d.58.26.5 — 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE

Domain ID domain_id	d1oj4b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.5 — GHMP Kinase, N-terminal domain

Domain ID domain_id	d1oj4b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.26 — GHMP Kinase, C-terminal domain
Family Family family	d.58.26.5 — 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE

CATH v4.4 (4 domains)

Domain ID domain_id	1oj4A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1oj4A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	890 — GHMP kinase, C-terminal domain

Domain ID domain_id	1oj4B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1oj4B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	890 — GHMP kinase, C-terminal domain

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Unit-cell length a length_a	61.000 Å
Unit-cell length b length_b	76.300 Å
Unit-cell length c length_c	68.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	65.940 Å
R factor r_factor	0.1674
R_work r_work	0.1655
R_free r_free	0.2024

Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

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

4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE

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

1oj4__assembly_1__model_1

1oj4__assembly_1__model_1 | I(q)

1oj4__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

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

4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE

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

1oj4__assembly_1__model_1

1oj4__assembly_1__model_1 | I(q)

1oj4__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)