2d45

Crystal structure of the MecI-mecA repressor-operator complex

Method: X-RAY DIFFRACTION

▼

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

Methicillin resistance regulatory protein mecI

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 4 DNA 4	5'-D(PTPAPCPTPAPCPAPTPAPTPGPTPAPGPTPA)-3' × 4 water × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MECI_STAAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 1–123 Author chain B； PDBConstruct 1–123； UniProt 1–123 Author chain C； PDBConstruct 1–123； UniProt 1–123 Author chain D； PDBConstruct 1–123； UniProt 1–123

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2d45
Deposition date deposition_date	2005-10-09
Structure title title	Crystal structure of the MecI-mecA repressor-operator complex
Keywords keywords	;METHICILLIN, B-LACTAM, Oligonucleotide binding domain, dimerization helical domain, repressor, pseudo-dyad DNA, protein-DNA complex, Transcription-DNA COMPLEX ;; Transcription/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2d45__assembly_1__model_1

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

Download this curve (.dat)

2d45__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d45__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.99 Å
Rg (electron density)	29.32 Å
Total Rg	30.13 Å
Atom count	5124
Residues	513
Excluded volume	88528 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d45__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	5'-D(PTPAPCPTPAPCPAPTPAPTPGPTPAPGPTPA)-3'
Molecular weight formula_weight	4896.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F,G,H
Atom count atom_count	5204

TACTACATATGTAGTA

Entity 2 Entity 2 polymer

Description description	Methicillin resistance regulatory protein mecI
Molecular weight formula_weight	14999.6 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

MDNKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNKK

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2d45a1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.39 — Penicillinase repressor

Domain ID domain_id	d2d45b1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.39 — Penicillinase repressor

Domain ID domain_id	d2d45c1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.39 — Penicillinase repressor

Domain ID domain_id	d2d45d1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.39 — Penicillinase repressor

CATH v4.4 (8 domains)

Domain ID domain_id	2d45A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2d45A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4040 — Penicillinase repressor fold
Homologous superfamily homologous superfamily	10 — Penicillinase repressor domain

Domain ID domain_id	2d45B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2d45B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4040 — Penicillinase repressor fold
Homologous superfamily homologous superfamily	10 — Penicillinase repressor domain

Domain ID domain_id	2d45C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2d45C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4040 — Penicillinase repressor fold
Homologous superfamily homologous superfamily	10 — Penicillinase repressor domain

Domain ID domain_id	2d45D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2d45D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4040 — Penicillinase repressor fold
Homologous superfamily homologous superfamily	10 — Penicillinase repressor domain

▶

Unit-cell length a length_a	61.464 Å
Unit-cell length b length_b	61.464 Å
Unit-cell length c length_c	419.777 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 32 1 2
Space-group number int_tables_number	153
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2670
R_work r_work	0.2640
R_free r_free	0.2970

Crystal structure of the MecI-mecA repressor-operator complex

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

Methicillin resistance regulatory protein mecI

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

2d45__assembly_1__model_1

2d45__assembly_1__model_1 | I(q)

2d45__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the MecI-mecA repressor-operator complex

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

Methicillin resistance regulatory protein mecI

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

2d45__assembly_1__model_1

2d45__assembly_1__model_1 | I(q)

2d45__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)