SAXSdb — 4c48

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

ACRIFLAVINE RESISTANCE PROTEIN B

ESCHERICHIA COLI K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	DARPIN × 3 UNCHARACTERIZED MEMBRANE PROTEIN YBHT × 3 （P0AAW9） DODECYL-BETA-D-MALTOSIDE × 27 NICKEL (II) ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACRB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1047； UniProt 1–1047

UNCHARACTERIZED MEMBRANE PROTEIN YBHT

Escherichia coli str. K-12 substr. W3110

UniProt P0AAW9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	ACRIFLAVINE RESISTANCE PROTEIN B × 3 （P31224） DARPIN × 3 DODECYL-BETA-D-MALTOSIDE × 27 NICKEL (II) ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBHT_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–49； UniProt 1–49

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	4c48
Deposition date deposition_date	2013-09-02
Structure title title	Crystal structure of AcrB-AcrZ complex
Keywords keywords	TRANSPORT PROTEIN, DRUG EFFLUX, TRANSMEMBRANE PROTEIN; TRANSPORT 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.

4c48__assembly_1__model_1

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

Download this curve (.dat)

4c48__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4c48__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.09 Å
Rg (electron density)	48.38 Å
Total Rg	48.62 Å
Atom count	28065
Residues	3690
Excluded volume	508040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4c48__assembly_1__model_1`	nonameric （9）	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	ACRIFLAVINE RESISTANCE PROTEIN B
Molecular weight formula_weight	113388.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9390

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVD

Source Source

Source organism organism	ESCHERICHIA COLI K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DARPIN
Molecular weight formula_weight	18317.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRGSHHHHHHGSDLGKKLLEAARAGRDDEVRILMANGADVNAADVVGWTPLHLAAYWGHLEIVEVLLKNGADVNAYDTLGSTPLHLAAHFGHLEIVEVLLKNGADVNAKDDNGITPLHLAANRGHLEIVEVLLKYGADVNAQDKFGKTAFDISINNGNEDLAEILQKLN

Source Source

Source organism organism	SYNTHETIC CONSTRUCT
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 3 Entity 3 polymer

Description description	UNCHARACTERIZED MEMBRANE PROTEIN YBHT
Molecular weight formula_weight	5304.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MLELLKSLVFAVIMVPVVMAIILGLIYGLGEVFNIFSGVGKKDQPGQNH

Source Source

Source organism organism	Escherichia coli str. K-12 substr. W3110
NCBI taxonomy ID ncbi_taxonomy_id	316407
Host organism host_organism	ESCHERICHIA COLI K-12

Entity 4 Entity 4 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 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	35

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	4c48A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	4c48A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	4c48A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1320 — Multidrug efflux transporter AcrB pore domain like

Domain ID domain_id	4c48A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

Domain ID domain_id	4c48A05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1640 — Multidrug efflux transporter AcrB transmembrane fold
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB transmembrane domain

Domain ID domain_id	4c48A06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1430 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	4c48A07
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1440 — Multidrug efflux transporter AcrB pore domain

Domain ID domain_id	4c48A08
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
Homologous superfamily homologous superfamily	10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains

Domain ID domain_id	4c48B00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	4c48C00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2480 —

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Unit-cell length a length_a	145.010 Å
Unit-cell length b length_b	145.010 Å
Unit-cell length c length_c	538.340 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	29.670 Å
R factor r_factor	0.2834
R_work r_work	0.2814
R_free r_free	0.3220

Crystal structure of AcrB-AcrZ complex

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

ACRIFLAVINE RESISTANCE PROTEIN B

State in the Current Structure

Other States of the Same Protein in the Database

UNCHARACTERIZED MEMBRANE PROTEIN YBHT

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

4c48__assembly_1__model_1

4c48__assembly_1__model_1 | I(q)

4c48__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

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 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of AcrB-AcrZ complex

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

ACRIFLAVINE RESISTANCE PROTEIN B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UNCHARACTERIZED MEMBRANE PROTEIN YBHT

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

4c48__assembly_1__model_1

4c48__assembly_1__model_1 | I(q)

4c48__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

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 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)