SAXSdb — 5mro

▼

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

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	Azolopyrimidine × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 ACETATE ION × 2 POTASSIUM ION × 2 CADMIUM ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPD_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–228； UniProt 76–302

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5mro
Deposition date deposition_date	2016-12-23
Structure title title	Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1)
Keywords keywords	herbicide, anti-infectives, drug discovery, allosteric inhibition, mutant, transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5mro__assembly_1__model_1

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

Download this curve (.dat)

5mro__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5mro__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.18 Å
Rg (electron density)	25.06 Å
Total Rg	26.15 Å
Atom count	3428
Residues	430
Excluded volume	62246 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5mro__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
Molecular weight formula_weight	25372.2 kDa
EC 编号 ec_number	2.7.7.60
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1848

MEKSVSVILLAGGQGKRMKMSMPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLAVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSEDS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	Azolopyrimidine
Molecular weight formula_weight	260.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	134

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5mroa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.13 — Cytidylytransferase

CATH v4.4 (1 domains)

Domain ID domain_id	5mroA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

▶

Unit-cell length a length_a	74.800 Å
Unit-cell length b length_b	74.800 Å
Unit-cell length c length_c	221.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2010
R_work r_work	0.1977
R_free r_free	0.2247

Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1)

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

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic

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

5mro__assembly_1__model_1

5mro__assembly_1__model_1 | I(q)

5mro__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1)

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

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic

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

5mro__assembly_1__model_1

5mro__assembly_1__model_1 | I(q)

5mro__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)