6grg

E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP and phosphate bound

Method: X-RAY DIFFRACTION

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

Bacteriocin microcin B17

Escherichia coli str. K-12 substr. MG1655

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Microcin B17-processing protein McbB × 4 （P23184） Microcin B17-processing protein McbC × 2 （P23185） Microcin B17-processing protein McbD × 2 （P23186） FLAVIN MONONUCLEOTIDE × 2 ZINC ION × 4 SULFATE ION × 2 GLYCEROL × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 1,2-ETHANEDIOL × 4 ADENOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 2 MAGNESIUM ION × 6 CHLORIDE ION × 2 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCBA_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–68； UniProt 1–69

Microcin B17-processing protein McbB

Escherichia coli str. K-12 substr. MG1655

UniProt P23184

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Bacteriocin microcin B17 × 2 （P05834） Microcin B17-processing protein McbC × 2 （P23185） Microcin B17-processing protein McbD × 2 （P23186） FLAVIN MONONUCLEOTIDE × 2 ZINC ION × 4 SULFATE ION × 2 GLYCEROL × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 1,2-ETHANEDIOL × 4 ADENOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 2 MAGNESIUM ION × 6 CHLORIDE ION × 2 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCBB_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 1； PDBConstruct 1–295； UniProt 1–295 Author chain 2； PDBConstruct 1–295； UniProt 1–295

Microcin B17-processing protein McbC

Escherichia coli str. K-12 substr. MG1655

UniProt P23185

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Bacteriocin microcin B17 × 2 （P05834） Microcin B17-processing protein McbB × 4 （P23184） Microcin B17-processing protein McbD × 2 （P23186） FLAVIN MONONUCLEOTIDE × 2 ZINC ION × 4 SULFATE ION × 2 GLYCEROL × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 1,2-ETHANEDIOL × 4 ADENOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 2 MAGNESIUM ION × 6 CHLORIDE ION × 2 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCBC_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–272； UniProt 1–272

Microcin B17-processing protein McbD

Escherichia coli str. K-12 substr. MG1655

UniProt P23186

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Bacteriocin microcin B17 × 2 （P05834） Microcin B17-processing protein McbB × 4 （P23184） Microcin B17-processing protein McbC × 2 （P23185） FLAVIN MONONUCLEOTIDE × 2 ZINC ION × 4 SULFATE ION × 2 GLYCEROL × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 1,2-ETHANEDIOL × 4 ADENOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 2 MAGNESIUM ION × 6 CHLORIDE ION × 2 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCBD_ECOLX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–396； UniProt 1–396

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	6grg
Deposition date deposition_date	2018-06-11
Structure title title	E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP and phosphate bound
Keywords keywords	microcin, DNA gyrase, heterocyclization, posttranslational modification, 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.

6grg__assembly_1__model_1

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

Download this curve (.dat)

6grg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6grg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.76 Å
Rg (electron density)	42.33 Å
Total Rg	42.65 Å
Atom count	20086
Residues	2494
Excluded volume	358410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6grg__assembly_1__model_1`	decameric （10）	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 (15)

Entity 1 Entity 1 polymer

Description description	Bacteriocin microcin B17
Molecular weight formula_weight	6853.4 kDa
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	10322

MGHHHHHHMELKASEFGVVLSVDALKLSRQSPLGVGIGGGGGGGGGGSCGGQGGGCGGCSNGCSGGNGGSGGSGSHI

Source Source

Source organism organism	Escherichia coli str. K-12 substr. MG1655
NCBI taxonomy ID ncbi_taxonomy_id	511145
Host organism host_organism	Escherichia coli BW25113

Entity 2 Entity 2 polymer

Description description	Microcin B17-processing protein McbB
Molecular weight formula_weight	34032.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2

MVLPDIKKGKDMINILPFEIISRNTKTLLITYISSVDITHEGMKKVLESLRSKQGIISEYLLDKLLDESLIDKDKGKEFLITTGVINKTKTSPLWVNSVIISDVPHLFSNAREQWKCDGVFVSHIIDIKDNNINVSDSTLIWLHLENYHSDIVKRIYSKFESNPGVAFIQSYYLKESFRIDGVYSPDLGTPCHFCHIERWLSREEKSFRRNEMSWANLLQLLKKYQMTLPALALGESERGFSYHLIKRRLQELTGTSLVKSHVDNFMSSVSADLITCILCKEPVIHWQACSCLER

Source Source

Source organism organism	Escherichia coli str. K-12 substr. MG1655
NCBI taxonomy ID ncbi_taxonomy_id	511145
Host organism host_organism	Escherichia coli BW25113

Entity 3 Entity 3 polymer

Description description	Microcin B17-processing protein McbC
Molecular weight formula_weight	30789.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSKHELSLVEVTHYTDPEVLAIVKDFHVRGNFASLPEFAERTFVSAVPLAHLEKFENKEVLFRPGFSSVINISSSHNFSRERLPSGINFCDKNKLSIRTIEKLLVNAFSSPDPGSVRRPYPSGGALYPIEVFLCRLSENTENWQAGTNVYHYLPLSQALEPVATCNTQSLYRSLSGGDSERLGKPHFALVYCIIFEKALFKYRYRGYRMALMETGSMYQNAVLVADQIGLKNRVWAGYTDSYVAKTMNLDQRTVAPLIVQFFGDVNDDKCLQ

Source Source

Source organism organism	Escherichia coli str. K-12 substr. MG1655
NCBI taxonomy ID ncbi_taxonomy_id	511145
Host organism host_organism	Escherichia coli BW25113

Entity 4 Entity 4 polymer

Description description	Microcin B17-processing protein McbD
Molecular weight formula_weight	44964.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MINVYSNLMSAWPATMAMSPKLNRNMPTFSQIWDYERITPASAAGETLKSIQGAIGEYFERRHFFNEIVTGGQKTLYEMMPPSAAKAFTEAFFQISSLTRDEIITHKFKTVRAFNLFSLEQQEIPAVIIALDNITAADDLKFYPDRDTCGCSFHGSLNDAIEGSLCEFMERQSLLLYWLQGKANTEISSEIVTGINHIDEILLALRSEGDIRIFDITLPGAPGHAVLTLYGTKNKISRIKYSTGLSYANSLKKALCKSVVELWQSYICLHNFLIGGYTDDDIIDSYQRHFMSCNKYESFTDLCENTVLLSDDVKLTLEENITSDTNLLNYLQQISDNIFVYYARERVSNSLVWYTKIVSPDFFLHMNNSGAININNKIYHTGDGIKVRESKMVPFP

Source Source

Source organism organism	Escherichia coli str. K-12 substr. MG1655
NCBI taxonomy ID ncbi_taxonomy_id	511145
Host organism host_organism	Escherichia coli BW25113

Entity 5 Entity 5 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 14 Entity 14 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	226

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Unit-cell length a length_a	180.640 Å
Unit-cell length b length_b	83.280 Å
Unit-cell length c length_c	86.790 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	86.760 Å
R factor r_factor	0.1683
R_work r_work	0.1653
R_free r_free	0.2259

E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP and phosphate bound

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

Bacteriocin microcin B17

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 B17-processing protein McbB

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 B17-processing protein McbC

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 B17-processing protein McbD

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

6grg__assembly_1__model_1

6grg__assembly_1__model_1 | I(q)

6grg__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 (15)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

Entity 15 Entity 15 water

7. Citations (1)