SAXSdb — 7phd

▼

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

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein

Streptomyces peucetius

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	SULFATE ION × 4 GLYCEROL × 3 S-ADENOSYLMETHIONINE × 2 ;methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I2N5E8_STRT9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 296–312； UniProt 295–311 Author chain B； PDBConstruct 296–312； UniProt 295–311

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein

Streptomyces peucetius

UniProt Q06528

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	SULFATE ION × 4 GLYCEROL × 3 S-ADENOSYLMETHIONINE × 2 ;methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNRK_STRPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–295； UniProt 2–285 Author chain A； PDBConstruct 313–369； UniProt 300–356 Author chain B； PDBConstruct 12–295； UniProt 2–285 Author chain B； PDBConstruct 313–369； UniProt 300–356

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	7phd
Deposition date deposition_date	2021-08-17
Structure title title	Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-decarboxylase TamK
Keywords keywords	;Carminomycin-4-O-methyltransferase variant; Chimeragenesis; tsukubarubicin 10-decarboxylase; Biosynthetic protein, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC PROTEIN
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.

7phd__assembly_1__model_1

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

Download this curve (.dat)

7phd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7phd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.52 Å
Rg (electron density)	28.92 Å
Total Rg	29.39 Å
Atom count	4943
Residues	641
Excluded volume	88343 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7phd__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 (6)

Entity 1 Entity 1 polymer

Description description	Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein
Molecular weight formula_weight	40144.6 kDa
EC 编号 ec_number	2.1.1.292
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	5280

MAHHHHHHHRSTAEPTVAARPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERAEAPSGGTRTSDLYFSVLDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPAATGA

Source Source

Source organism organism	Streptomyces peucetius
NCBI taxonomy ID ncbi_taxonomy_id	1950
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate ;
Molecular weight formula_weight	569.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	334

▶

Unit-cell length a length_a	60.509 Å
Unit-cell length b length_b	101.321 Å
Unit-cell length c length_c	62.968 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.29 °
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	monoclinic

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	48.040 Å
R factor r_factor	0.2209
R_work r_work	0.2205
R_free r_free	0.2379

Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-decarboxylase TamK

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

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein

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

7phd__assembly_1__model_1

7phd__assembly_1__model_1 | I(q)

7phd__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 (6)

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 water

7. Citations (1)

Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-decarboxylase TamK

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

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein

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

7phd__assembly_1__model_1

7phd__assembly_1__model_1 | I(q)

7phd__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 (6)

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 water

7. Citations (1)