SAXSdb — 2vde

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

OUTER MEMBRANE PROTEIN TOLC

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–450 Chain B； UniProt 1–450 Chain C； UniProt 1–450	Fragment：RESIDUES 1-450 Mutation：YES	CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 10.5；PROTEIN WAS CRYSTALLIZED FROM 0.1M CAPS PH10.5, 30% PEG400	Resolution 3.20 Å R-free 0.315

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 2VDE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EK9 2.1A X-RAY STRUCTURE OF TOLC: AN INTEGRAL OUTER MEMBRANE PROTEIN AND EFFLUX PUMP COMPONENT FROM ESCHERICHIA COLI Deposited 2000-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 25–452（428 aa） Chain B 25–452（428 aa） Chain C 25–452（428 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 2000 MME, PEG 400, Sodium Chloride, Magnesium Chloride, dodecyl glucopyrsanoside, hexyl glucopyranoside, heptyl gluocopyranoside, octyl glucopyranoside, 1,2,3-heptanetriol, Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.257
1TQQ Structure of TolC in complex with hexamminecobalt Deposited 2004-06-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 25–495（471 aa） Chain B 25–495（471 aa） Chain C 25–495（471 aa）	Not recorded	NCO COBALT HEXAMMINE(III) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；0.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% polyethylene glycol 2000 monomethyl ether, 10% polyethylene glycol 400, 10mM NaCl, 20mM MgCl2, 20mM Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.75 Å R-free 0.305
2VDD Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps Deposited 2007-10-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–450（450 aa） Fragment：RESIDUES 1-450 Chain B 1–450（450 aa） Fragment：RESIDUES 1-450 Chain C 1–450（450 aa） Fragment：RESIDUES 1-450	Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 3 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLISED FROM 0.1M HEPES 7.5, 5% ISOPROPANOL, 10% PEG4000	Resolution 3.30 Å R-free 0.295
2WMZ Structure of a mutated TolC Deposited 2009-07-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450 Chain B 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450 Chain C 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450	Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 3 PGE TRIETHYLENE GLYCOL × 5 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；50 MM TRIS PH 8.2, 50 MM NACL, 14% PEG2000, 0.075% N-DODECYL-BETA-D-MALTOSIDE, 0.3% N-OCTYL BETA-D-GLUCOPYRANOSIDE	Resolution 2.90 Å R-free 0.301
2XMN High resolution snapshots of defined TolC open states present an iris- like movement of periplasmic entrance helices Deposited 2010-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 23–450（428 aa） Fragment：RESIDUES 23-450 Chain B 23–450（428 aa） Fragment：RESIDUES 23-450 Chain C 23–450（428 aa） Fragment：RESIDUES 23-450	Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 3 LMT DODECYL-BETA-D-MALTOSIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；PH 7.4	Resolution 2.85 Å R-free 0.309
5NG5 multi-drug efflux; membrane transport; RND superfamily; Drug resistance Deposited 2017-03-16	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 × 15 PDB declaration: pentadecameric	Chain C 1–493（493 aa） Chain F 1–493（493 aa） Chain I 1–493（493 aa）	Not recorded	5QF 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)	Resolution 6.50 Å
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 23–493（471 aa） Chain B 23–493（471 aa） Chain C 23–493（471 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 23–493（471 aa） Chain B 23–493（471 aa） Chain C 23–493（471 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
5O66 Asymmetric AcrABZ-TolC Deposited 2017-06-05	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 × 15 PDB declaration: pentadecameric	Chain A 1–493（493 aa） Chain B 1–493（493 aa） Chain C 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
5V5S multi-drug efflux; membrane transport; RND superfamily; Drug resistance Deposited 2017-03-15	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 × 12 PDB declaration: dodecameric	Chain A 23–464（442 aa） Chain B 23–464（442 aa） Chain C 23–464（442 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)	Resolution 6.50 Å
6WXH Colicin E1 fragment in nanodisc-embedded TolC Deposited 2020-05-10	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 × 4 PDB declaration: tetrameric	Chain A 1–493（493 aa） Chain B 1–493（493 aa） Chain C 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
6WXI Colicin E1 fragment in nanodisc-embedded TolC Deposited 2020-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–493（493 aa） Chain B 1–493（493 aa） Chain C 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å
8ZAL EmrAB-TolC MFS-type tripartite multidrug efflux pump EA Deposited 2024-04-25	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 × 10 PDB declaration: decameric	Chain G 23–450（428 aa） Chain H 23–450（428 aa） Chain I 23–450（428 aa）	Mutation：V169L Mutation：V169L Mutation：V169L	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8ZAR EmrAB-TolC MFS-type tripartite multidrug efflux pump FA Deposited 2024-04-25	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 × 10 PDB declaration: decameric	Chain G 1–493（493 aa） Chain H 1–493（493 aa） Chain I 1–493（493 aa）	Mutation：V191L Mutation：V191L Mutation：V191L	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 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 A 23–493（471 aa） Chain B 23–493（471 aa） Chain C 23–493（471 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
9TG4 Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump Deposited 2025-11-28	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 × 18 PDB declaration: 18-meric	Chain A 23–493（471 aa） Chain B 23–493（471 aa） Chain C 23–493（471 aa）	Not recorded	CL CHLORIDE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9V52 Structure of TolC and YbjP closed state complex Deposited 2025-05-25	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 × 6 PDB declaration: hexameric	Chain C1 1–493（493 aa） Chain C2 1–493（493 aa） Chain C3 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.56 Å
9V53 Structure of TolC, YbjP, and AcrABZ complex Deposited 2025-05-25	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 × 18 PDB declaration: octadecameric	Chain C1 1–493（493 aa） Chain C2 1–493（493 aa） Chain C3 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.39 Å
9V55 Structure of TolC, YbjP, and AcrA complex Deposited 2025-05-25	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 × 12 PDB declaration: dodecameric	Chain C1 1–493（493 aa） Chain C2 1–493（493 aa） Chain C3 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.26 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOLC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–450； UniProt 1–450 Author chain B； PDBConstruct 1–450； UniProt 1–450 Author chain C； PDBConstruct 1–450； UniProt 1–450

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	2vde
Deposition date deposition_date	2007-10-04
Structure title title	Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps
Keywords keywords	;OUTER MEMBRANE, ALPHA HELICAL BARREL, TRANSPORT PROTEIN, MULTIDRUG EFFLUX PUMP, INTEGRAL MEMBRANE PROTEIN, MEMBRANE, TRANSPORT, BETA BARREL, TRANSMEMBRANE ;; TRANSPORT 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	41.25 Å
Radius of gyration Rg (electron density) rg_electron	41.20 Å
Forward intensity I(0) i0	330136000.00
Molecular weight molecular_weight	140880.0 kDa
Excluded volume excluded_volume	174120 Å³
Envelope volume envelope_volume	265060 Å³
Hydration-shell volume shell_volume	58176 Å³
Envelope diameter envelope_diameter	152.6 Å
Shell Rg shell_rg	43.02 Å
Envelope Rg envelope_rg	40.39 Å
Shape Rg shape_rg	41.20 Å
Total Rg total_rg	41.30 Å
Total atoms total_atoms	9913
Residues n_residues	1287
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	143.4 Å
Rg (real space) rg_real	41.59 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	3.3010e+08
I(0) uncertainty (real space) i0_real_error	5.3340e+06
Rg (reciprocal space) rg_reciprocal	41.25 Å
I(0) (reciprocal space) i0_reciprocal	330000000.0000
Solution quality estimate total_estimate	0.7839
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.3 Å
Skewness Skewness skewness	0.687
Kurtosis Kurtosis kurtosis	0.137
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39390000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.564; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.502

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	OUTER MEMBRANE PROTEIN TOLC
Molecular weight formula_weight	50623.0 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9921

MRKLLPILIGLSLSGFSSLSQAENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANELTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGFSVGTETIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPELEHHHHHHHH

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2vdeA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	2vdeB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	2vdeC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

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8. Citations (1)

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Unit-cell length a length_a	128.284 Å
Unit-cell length b length_b	136.176 Å
Unit-cell length c length_c	136.133 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	22.080 Å
R factor r_factor	0.2680
R_work r_work	0.2660
R_free r_free	0.3150

fit	/app/data/saxs_computation/vd/2vde/2vde.fit
pddf	/app/data/pr_computation/vd/2vde/2vde.pr.out
profile	/app/data/saxs_computation/vd/2vde/2vde.dat

Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps

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

OUTER MEMBRANE PROTEIN TOLC

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