SAXSdb — 3h9j

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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 4	Microcin C7 ANALOG × 2 （Q47505） ZINC ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Microcin C7 ANALOG × 2 （Q47505） ZINC ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 3 water × 3	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 4–353； UniProt 1–350 Author chain B； PDBConstruct 4–353； UniProt 1–350 Author chain C； PDBConstruct 4–353； UniProt 1–350 Author chain D； PDBConstruct 4–353； UniProt 1–350

Microcin C7 ANALOG

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 4	MccB protein × 2 （Q47506） ZINC ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	MccB protein × 2 （Q47506） ZINC ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 3 water × 3	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 E； PDBConstruct 1–7； UniProt 1–7 Author chain F； PDBConstruct 1–7； UniProt 1–7 Author chain G； PDBConstruct 1–7； UniProt 1–7 Author chain H； 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	3h9j
Deposition date deposition_date	2009-04-30
Structure title title	Crystal structure of E. coli MccB + AMPCPP + SeMeT MccA
Keywords keywords	;Ubiquitin-activating enzyme, microcin, bacteriocin, Mcc7, peptide antibiotic, N-P bond formation, Antibiotic, Antimicrobial, Formylation, Phosphoprotein, TRANSFERASE, TRANSFERASE-ANTIBIOTIC COMPLEX ;; TRANSFERASE/ANTIBIOTIC
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.

3h9j__assembly_1__model_1

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

Download this curve (.dat)

3h9j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3h9j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.12 Å
Rg (electron density)	26.30 Å
Total Rg	27.03 Å
Atom count	5270
Residues	675
Excluded volume	93732 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3h9j__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3h9j__assembly_2__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	MccB protein
Molecular weight formula_weight	39409.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10848

GSHMDYILGRYVKIARYGSGGLVGGGGKEQYVENLVLWENIIKTAYCFITPSSYTAALETANIPEKDFSNCFRFLKENFFIIPGEYNNSTENNRYSRNFLHYQSYGANPVLVQDKLKNAKVVILGCGGIGNHVSVILATSGIGEIILIDNDQIENTNLTRQVLFSEDDVGKNKTEVIKRELLKRNSEISVSEIALNINDYTDLHKVPEADIWVVSADHPFNLINWVNKYCVRANQPYINAGYVNDIAVFGPLYVPGKTGCYECQKVVADLYGSEKENIDHKIKLINSRFKPATFAPVNNVAAALCAADVIKFIGKYSEPLSLNKRIGIWSDEIKIHSQNMGRSPVCSVCGNRM

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 ANALOG
Molecular weight formula_weight	810.7 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MRTGNAN

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	5

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	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3h9jA01
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	3h9jA02
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	3h9jB01
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	3h9jB02
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	3h9jC01
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	3h9jC02
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	3h9jD01
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	3h9jD02
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	55.841 Å
Unit-cell length b length_b	138.004 Å
Unit-cell length c length_c	80.816 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	39.970 Å
R factor r_factor	0.1990
R_work r_work	0.1960
R_free r_free	0.2550

Crystal structure of E. coli MccB + AMPCPP + SeMeT 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 ANALOG

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

3h9j__assembly_1__model_1

3h9j__assembly_1__model_1 | I(q)

3h9j__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 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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of E. coli MccB + AMPCPP + SeMeT 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 ANALOG

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

3h9j__assembly_1__model_1

3h9j__assembly_1__model_1 | I(q)

3h9j__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 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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)