SAXSdb — 3t5m

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

Microcin immunity protein MccF

Bacillus anthracis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE MONOPHOSPHATE × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q81RT8_BACAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–336； UniProt 1–333 Author chain B； PDBConstruct 4–336； UniProt 1–333

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	3t5m
Deposition date deposition_date	2011-07-27
Structure title title	Crystal structure of the S112A mutant of mycrocine immunity protein (MccF) with AMP
Keywords keywords	MccF, AMP, CSGID, Structural Genomics, Center for Structural Genomics of Infectious Diseases, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

3t5m__assembly_1__model_1

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

Download this curve (.dat)

3t5m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3t5m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.56 Å
Rg (electron density)	25.81 Å
Total Rg	26.59 Å
Atom count	5317
Residues	668
Excluded volume	95053 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3t5m__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Microcin immunity protein MccF
Molecular weight formula_weight	38007.3 kDa
Mutation mutation	S112A
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	5960

SNAMPLPKSLKYGDTIGIYSPSSPVTYTSPKRFERAKSYLLQKGFHILEGSLTGRYDYYRSGSIQERAKELNALIRNPNVSCIMSTIGGMNSNSLLPYIDYDAFQNNPKIMIGYADATALLLGIYAKTGIPTFYGPALVPSFGEFEPFVDDTYKYFLETLLHDQALPYNIKQPLFWSDEFINWEEKTKEKELRPNNWISVTNGQATGRVIGGNLNTIQGIWGSPYMPCIQEGDILFIEDSSKDAATIERSFSFLKINGVFDKVSGIILGKHEQFDDCGTNRKPYEILLEVLQNQRIPLLADFDCCHTHPMITMPIGVQVKMDATNKTIHILEKWKI

Source Source

Source organism organism	Bacillus anthracis
Common name common_name	anthrax,anthrax bacterium
NCBI taxonomy ID ncbi_taxonomy_id	198094
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	628

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3t5mA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10740 — Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain

Domain ID domain_id	3t5mA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	60 — LD-carboxypeptidase A C-terminal domain-like

Domain ID domain_id	3t5mB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10740 — Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain

Domain ID domain_id	3t5mB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	60 — LD-carboxypeptidase A C-terminal domain-like

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Unit-cell length a length_a	118.389 Å
Unit-cell length b length_b	118.389 Å
Unit-cell length c length_c	55.764 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.749 Å
Low-resolution limit resolution_low	28.714 Å
R factor r_factor	0.1861
R_work r_work	0.1852
R_free r_free	0.2020

Crystal structure of the S112A mutant of mycrocine immunity protein (MccF) with AMP

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

Microcin immunity protein MccF

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

3t5m__assembly_1__model_1

3t5m__assembly_1__model_1 | I(q)

3t5m__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the S112A mutant of mycrocine immunity protein (MccF) with AMP

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

Microcin immunity protein MccF

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

3t5m__assembly_1__model_1

3t5m__assembly_1__model_1 | I(q)

3t5m__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)