SAXSdb — 3fpp

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

Macrolide-specific efflux protein macA

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 31–371 Chain B； UniProt 31–371	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；1M potassium sodium tartrate tetrahydrate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.99 Å R-free 0.349

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3FPP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5NIK Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump Deposited 2017-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–371（371 aa） Chain E 1–371（371 aa） Chain F 1–371（371 aa） Chain G 1–371（371 aa） Chain H 1–371（371 aa） Chain I 1–371（371 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
5NIL Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section Deposited 2017-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–371（371 aa） Chain E 1–371（371 aa） Chain F 1–371（371 aa） Chain G 1–371（371 aa） Chain H 1–371（371 aa） Chain I 1–371（371 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å
9QGY Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump Deposited 2025-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain G 1–371（371 aa） Chain H 1–371（371 aa） Chain I 1–371（371 aa） Chain J 1–371（371 aa） Chain K 1–371（371 aa） Chain L 1–371（371 aa）	Not recorded	CL CHLORIDE ION × 3 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.48 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MACA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–341； UniProt 31–371 Author chain B； PDBConstruct 1–341； UniProt 31–371

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	3fpp
Deposition date deposition_date	2009-01-06
Structure title title	Crystal structure of E.coli MacA
Keywords keywords	;Hexameric assembly, membrane fusion protein, drug efflux pump, periplasmic protein, Antibiotic resistance, Cell inner membrane, Cell membrane, Membrane, Transport, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.47 Å
Radius of gyration Rg (electron density) rg_electron	37.64 Å
Forward intensity I(0) i0	54738500.00
Molecular weight molecular_weight	58366.0 kDa
Excluded volume excluded_volume	73194 Å³
Envelope volume envelope_volume	105410 Å³
Hydration-shell volume shell_volume	26710 Å³
Envelope diameter envelope_diameter	137.6 Å
Shell Rg shell_rg	37.32 Å
Envelope Rg envelope_rg	38.10 Å
Shape Rg shape_rg	37.66 Å
Total Rg total_rg	37.57 Å
Total atoms total_atoms	4097
Residues n_residues	533
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	131.5 Å
Rg (real space) rg_real	38.04 Å
Rg uncertainty (real space) rg_real_error	1.83 Å
I(0) (real space) i0_real	5.4740e+07
I(0) uncertainty (real space) i0_real_error	1.0700e+06
Rg (reciprocal space) rg_reciprocal	37.69 Å
I(0) (reciprocal space) i0_reciprocal	54720000.0000
Solution quality estimate total_estimate	0.8023
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.3 Å
Skewness Skewness skewness	0.535
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3293000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.551; Smooth: 0.781

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3fppA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	170 — Efflux pump adaptor protein, beta barrel domain

Domain ID domain_id	3fppA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3fppA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1990 —

Domain ID domain_id	3fppB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	170 — Efflux pump adaptor protein, beta barrel domain

Domain ID domain_id	3fppB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3fppB03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1990 —

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8. Citations (1)

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Unit-cell length a length_a	128.517 Å
Unit-cell length b length_b	128.517 Å
Unit-cell length c length_c	110.311 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	12

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.990 Å
Low-resolution limit resolution_low	49.690 Å
R factor r_factor	0.2830
R_work r_work	0.2830
R_free r_free	0.3490

Description description	Macrolide-specific efflux protein macA
Molecular weight formula_weight	37187.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4097

Crystal structure of E.coli MacA

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

Macrolide-specific efflux protein macA

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/fp/3fpp/3fpp.fit
pddf	/app/data/pr_computation/fp/3fpp/3fpp.pr.out
profile	/app/data/saxs_computation/fp/3fpp/3fpp.dat