3d19

Crystal structure of a conserved metalloprotein from Bacillus cereus

Method: X-RAY DIFFRACTION

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

Conserved metalloprotein

Bacillus cereus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 6 FE (III) ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4MW04_BACCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–275； UniProt 11–282 Author chain B； PDBConstruct 4–275； UniProt 11–282 Author chain C； PDBConstruct 4–275； UniProt 11–282 Author chain D； PDBConstruct 4–275； UniProt 11–282 Author chain E； PDBConstruct 4–275； UniProt 11–282 Author chain F； PDBConstruct 4–275； UniProt 11–282

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	3d19
Deposition date deposition_date	2008-05-05
Structure title title	Crystal structure of a conserved metalloprotein from Bacillus cereus
Keywords keywords	;STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, Protein Structure Initiative, NYSGXRC, New York SGX Research Center for Structural Genomics ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

3d19__assembly_1__model_1

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

Download this curve (.dat)

3d19__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d19__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.40 Å
Rg (electron density)	36.57 Å
Total Rg	37.04 Å
Atom count	12920
Residues	1558
Excluded volume	230150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d19__assembly_1__model_1`	hexameric （6）	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	Conserved metalloprotein
Molecular weight formula_weight	33339.0 kDa
Mutation mutation	L39F, M137I, E138Q, A193E, V211A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	13109

MSLDTGVTSVMFVERSLNEIRFWSRIMKEHSFFLRLGFRCEDTQLIEEANQFYRLFEHIEQIAHSYTNETDPEQIKRFNAEVQQAATNIWGFKRKILGLILTCKLPGQNNFPLLVDHTSREADYFRKRLIQLNEGKLDALPDAIIKENVFFLRIMADHAKFIGHLLDPSERKLVDTARNFSNDFDELMYQAIDLESMKPQSQTAPLLDQFLDQNRVSVASLRDFKKTARDLIEQCKIKSIIHPLLADHVFREADRFLEIIDMYDVHLTNIQSQPREGHHHHHH

Source Source

Source organism organism	Bacillus cereus
NCBI taxonomy ID ncbi_taxonomy_id	269801
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3d19a1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19a2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19b1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19b2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19c1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19c2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19d1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19d2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19e1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19e2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19f1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

Domain ID domain_id	d3d19f2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.13 — Bacillus cereus metalloprotein-like
Family Family family	a.29.13.1 — Bacillus cereus metalloprotein-like

CATH v4.4 (6 domains)

Domain ID domain_id	3d19A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	120 — Protein of unknown function DUF2935

Domain ID domain_id	3d19B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	120 — Protein of unknown function DUF2935

Domain ID domain_id	3d19C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	120 — Protein of unknown function DUF2935

Domain ID domain_id	3d19D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	120 — Protein of unknown function DUF2935

Domain ID domain_id	3d19E00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	120 — Protein of unknown function DUF2935

Domain ID domain_id	3d19F00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	120 — Protein of unknown function DUF2935

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Unit-cell length a length_a	74.825 Å
Unit-cell length b length_b	136.378 Å
Unit-cell length c length_c	87.060 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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	20.000 Å
R factor r_factor	0.2100
R_work r_work	0.2060
R_free r_free	0.2680

Crystal structure of a conserved metalloprotein from Bacillus cereus

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

Conserved metalloprotein

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

3d19__assembly_1__model_1

3d19__assembly_1__model_1 | I(q)

3d19__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of a conserved metalloprotein from Bacillus cereus

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

Conserved metalloprotein

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

3d19__assembly_1__model_1

3d19__assembly_1__model_1 | I(q)

3d19__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)