SAXSdb — 6om4

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

MccB protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Microcin C7 × 1 （Q47505） ZINC ION × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Microcin C7 × 1 （Q47505） ZINC ION × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q47506_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–348； UniProt 1–348 Author chain B； PDBConstruct 1–348； UniProt 1–348

Microcin C7

OrganismNot specified

UniProt Q47505

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	MccB protein × 1 （Q47506） ZINC ION × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	MccB protein × 1 （Q47506） ZINC ION × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCCC7_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–7； UniProt 1–7 Author chain D； PDBConstruct 1–7； UniProt 1–7

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	6om4
Deposition date deposition_date	2019-04-18
Structure title title	The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA
Keywords keywords	Microcin C7, phosphoramidate, Trojan Horse Antibiotic, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

6om4__assembly_1__model_1

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

Download this curve (.dat)

6om4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6om4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.82 Å
Rg (electron density)	24.34 Å
Total Rg	25.01 Å
Atom count	2801
Residues	351
Excluded volume	49794 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6om4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6om4__assembly_2__model_1`	dimeric （2）	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 (7)

Entity 1 Entity 1 polymer

Description description	MccB protein
Molecular weight formula_weight	38853.1 kDa
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	6027

MDYILGRYVKIARYGSGGLVGGGGKEQYVENLVLWENIIKTAYCFITPSSYTAALETANIPEKDFSNCFRFLKENFFIIPSEYNNSTENNRYSRNFLHYQSYGANPVLVQDKLKNAKVVILGCGGIGNHVSVILATSGIGEIILIDNDQIENTNLTRQVLFSEDDVGKNKTEVIKRELLKRNSEISVSEIALNINDYTDLHKVPEADIWVVSADHPFNLINWVNKYCVRANQPYINAGYVNDIAVFGPLYVPGKTGCYECQKVVADLYGAEKENIDHKIKLINSRFKPATFAPVNNVAAALCAADVIKFIGKYSEPLSLNKRIGIWSDEIKIHSQNMGRSPVCSVCGN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Microcin C7
Molecular weight formula_weight	792.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MRTGNAD

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine
Molecular weight formula_weight	346.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	439

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6om4A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	6om4A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	6om4B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	6om4B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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Unit-cell length a length_a	55.094 Å
Unit-cell length b length_b	76.059 Å
Unit-cell length c length_c	131.902 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	65.980 Å
R factor r_factor	0.1569
R_work r_work	0.1547
R_free r_free	0.1987

The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA

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

MccB protein

State in the Current Structure

Other States of the Same Protein in the Database

Microcin C7

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

6om4__assembly_1__model_1

6om4__assembly_1__model_1 | I(q)

6om4__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 polymer

Polymer 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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA

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

MccB 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

Microcin C7

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

6om4__assembly_1__model_1

6om4__assembly_1__model_1 | I(q)

6om4__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 polymer

Polymer 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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)