SAXSdb — 6qgy

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

Outer membrane protein assembly factor BamA

Escherichia coli O157:H7

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 421–810	Not recorded	NanoB12 × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；32% PEG 400, 0.2 M ammonium phosphate, 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 4.5	Resolution 2.51 Å R-free 0.244
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 421–810	Not recorded	NanoB12 × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；32% PEG 400, 0.2 M ammonium phosphate, 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 4.5	Resolution 2.51 Å R-free 0.244

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 6QGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6FSU Crystal structure of E.coli BamA beta-barrel with a C-terminal extension Deposited 2018-02-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 421–810（390 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22 % (w/v) PEG 400, 0.07 M NaCl, 0.05 M sodium citrate pH 4.5	Resolution 2.60 Å R-free 0.298
6FSU Crystal structure of E.coli BamA beta-barrel with a C-terminal extension Deposited 2018-02-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 421–810（390 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22 % (w/v) PEG 400, 0.07 M NaCl, 0.05 M sodium citrate pH 4.5	Resolution 2.60 Å R-free 0.298
6QGW Crystal structure of E.coli BamA beta-barrel in complex with nanobody E6 Deposited 2019-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 421–810（390 aa）	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5	Resolution 1.94 Å R-free 0.230
6QGX Crystal structure of E.coli BamA beta-barrel in complex with nanobody F7 Deposited 2019-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 421–810（390 aa）	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；33% PEG 400, 0.23 M NaCl, 0.05 M sodium acetate	Resolution 2.20 Å R-free 0.266
7NRE Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 1) Deposited 2021-03-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 421–810（390 aa）	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.06 M Magnesium chloride/Calcium Chloride, 0.1 M imidazole/2-(N-morpholino)ethanesulfonic acid pH 6.5, 12.5% v/v 2-Methyl-2,4-pentanediol, 12.5% w/v Polyethylene glycol 1,000, and 12.5% w/v Polyethylene glycol 3,350	Resolution 2.30 Å R-free 0.232
7NRF Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2) Deposited 2021-03-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 421–810（390 aa）	Not recorded	MG MAGNESIUM ION × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Magnesium chloride, 0.03 M Tris pH 8.0, 19% w/v Polyethylene glycol 4,000	Resolution 2.20 Å R-free 0.232
7P1C Crystal structure of E.coli BamA beta-barrel in complex with darobactin B Deposited 2021-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 419–810（392 aa）	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Calcium chloride dihydrate, 0.1M HEPES 7.5, 53% v/v PEG 400	Resolution 2.50 Å R-free 0.249
7R1V Crystal structure of E.coli BamA beta-barrel in complex with dynobactin A Deposited 2022-02-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 421–810（390 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.12 M lithium sulfate, 0.02 M Tris pH7.5, 0.1 M sodium citrate pH 5.0, and 20% (v/v) PEG300	Resolution 2.50 Å R-free 0.275

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BAMA_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–411； UniProt 421–810 Author chain C； PDBConstruct 22–411； UniProt 421–810

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	6qgy
Deposition date deposition_date	2019-01-14
Structure title title	Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12
Keywords keywords	Beta-Barrel, outer membrane, protein insertion, protein folding, protein maturation, 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	37.11 Å
Radius of gyration Rg (electron density) rg_electron	36.77 Å
Forward intensity I(0) i0	192325000.00
Molecular weight molecular_weight	110740.0 kDa
Excluded volume excluded_volume	137750 Å³
Envelope volume envelope_volume	189530 Å³
Hydration-shell volume shell_volume	44176 Å³
Envelope diameter envelope_diameter	124.8 Å
Shell Rg shell_rg	42.04 Å
Envelope Rg envelope_rg	35.72 Å
Shape Rg shape_rg	36.74 Å
Total Rg total_rg	37.24 Å
Total atoms total_atoms	15170
Residues n_residues	982
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	119.7 Å
Rg (real space) rg_real	37.15 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	1.9230e+08
I(0) uncertainty (real space) i0_real_error	3.4810e+06
Rg (reciprocal space) rg_reciprocal	37.13 Å
I(0) (reciprocal space) i0_reciprocal	192300000.0000
Solution quality estimate total_estimate	0.8871
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.2 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.721
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21190000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.876

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Outer membrane protein assembly factor BamA
Molecular weight formula_weight	46022.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	15487

MGSSHHHHHHSSGENLYFQHMRNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYESATQDGAKDLSKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

来源 Source

来源生物 organism	Escherichia coli O157:H7
NCBI Class编号 ncbi_taxonomy_id	83334
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	NanoB12
Molecular weight formula_weight	13637.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SQGQLVESGGGMVQAGGSLRLSCAASGRTFNGWTAAWFRQAPGKDREFVAAISRSGDYTYYTNSVKGRFTISRDSAKNNLYLQMDSLKPEDTAVYYCAAKTGTWATMDRRYDYWGQGTRVTVSA

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	317

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6qgyb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6qgyd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (2 domains)

Domain ID domain_id	6qgyA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	50 — membrane protein fhac: a member of the omp85/tpsb transporter family

Domain ID domain_id	6qgyC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	50 — membrane protein fhac: a member of the omp85/tpsb transporter family

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8. Citations (1)

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Unit-cell length a length_a	99.709 Å
Unit-cell length b length_b	86.664 Å
Unit-cell length c length_c	125.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.509 Å
Low-resolution limit resolution_low	48.484 Å
R factor r_factor	0.2235
R_work r_work	0.2224
R_free r_free	0.2442

fit	/app/data/saxs_computation/qg/6qgy/6qgy.fit
pddf	/app/data/pr_computation/qg/6qgy/6qgy.pr.out
profile	/app/data/saxs_computation/qg/6qgy/6qgy.dat

Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12

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

Outer membrane protein assembly factor BamA

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)