6gri

E. coli Microcin synthetase McbBCD complex

Method: X-RAY DIFFRACTION

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

Microcin B17-processing protein McbB

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Microcin B17-processing protein McbC × 2 （P23185） Microcin B17-processing protein McbD × 2 （P23186） ZINC ION × 4 SULFATE ION × 4 CHLORIDE ION × 6 FLAVIN MONONUCLEOTIDE × 2 water × 8	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	1
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

UniProt P23185

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Microcin B17-processing protein McbB × 4 （P23184） Microcin B17-processing protein McbD × 2 （P23186） ZINC ION × 4 SULFATE ION × 4 CHLORIDE ION × 6 FLAVIN MONONUCLEOTIDE × 2 water × 8	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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–272； UniProt 1–272

Microcin B17-processing protein McbD

Escherichia coli

UniProt P23186

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Microcin B17-processing protein McbB × 4 （P23184） Microcin B17-processing protein McbC × 2 （P23185） ZINC ION × 4 SULFATE ION × 4 CHLORIDE ION × 6 FLAVIN MONONUCLEOTIDE × 2 water × 8	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	3
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	6gri
Deposition date deposition_date	2018-06-11
Structure title title	E. coli Microcin synthetase McbBCD complex
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.

6gri__assembly_1__model_1

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

Download this curve (.dat)

6gri__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6gri__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.62 Å
Rg (electron density)	42.21 Å
Total Rg	42.43 Å
Atom count	18594
Residues	2414
Excluded volume	329750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6gri__assembly_1__model_1`	octameric （8）	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 (8)

Entity 1 Entity 1 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
Atom count atom_count	9354

MVLPDIKKGKDMINILPFEIISRNTKTLLITYISSVDITHEGMKKVLESLRSKQGIISEYLLDKLLDESLIDKDKGKEFLITTGVINKTKTSPLWVNSVIISDVPHLFSNAREQWKCDGVFVSHIIDIKDNNINVSDSTLIWLHLENYHSDIVKRIYSKFESNPGVAFIQSYYLKESFRIDGVYSPDLGTPCHFCHIERWLSREEKSFRRNEMSWANLLQLLKKYQMTLPALALGESERGFSYHLIKRRLQELTGTSLVKSHVDNFMSSVSADLITCILCKEPVIHWQACSCLER

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BW25113

Entity 2 Entity 2 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
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BW25113

Entity 3 Entity 3 polymer

Description description	Microcin B17-processing protein McbD
Molecular weight formula_weight	44964.0 kDa
Mutation mutation	There is a T171R substitution relative to UniProtKB sequence
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
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BW25113

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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Unit-cell length a length_a	183.900 Å
Unit-cell length b length_b	82.110 Å
Unit-cell length c length_c	87.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.45 °
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	2.700 Å
Low-resolution limit resolution_low	91.920 Å
R factor r_factor	0.1900
R_work r_work	0.1865
R_free r_free	0.2548

E. coli Microcin synthetase McbBCD complex

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

Microcin B17-processing protein McbB

State in the Current Structure

Other States of the Same Protein in the Database

Microcin B17-processing protein McbC

State in the Current Structure

Other States of the Same Protein in the Database

Microcin B17-processing protein McbD

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

6gri__assembly_1__model_1

6gri__assembly_1__model_1 | I(q)

6gri__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

E. coli Microcin synthetase McbBCD complex

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

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

6gri__assembly_1__model_1

6gri__assembly_1__model_1 | I(q)

6gri__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)