SAXSdb — 7nrf

▼

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	Darobactin × 1 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

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 7NRF	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
6QGY Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12 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 × 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
6QGY Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12 Deposited 2019-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 421–810（390 aa）	Not recorded	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
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
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 9 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

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	7nrf
Deposition date deposition_date	2021-03-03
Structure title title	Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2)
Keywords keywords	;Beta-Barrel, outer membrane, protein insertion, protein folding, protein maturation, antibiotic, natural product, cyclized peptide, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.78 Å
Radius of gyration Rg (electron density) rg_electron	22.36 Å
Forward intensity I(0) i0	31166800.00
Molecular weight molecular_weight	43612.0 kDa
Excluded volume excluded_volume	54731 Å³
Envelope volume envelope_volume	68474 Å³
Hydration-shell volume shell_volume	25714 Å³
Envelope diameter envelope_diameter	74.8 Å
Shell Rg shell_rg	29.43 Å
Envelope Rg envelope_rg	22.18 Å
Shape Rg shape_rg	22.36 Å
Total Rg total_rg	23.27 Å
Total atoms total_atoms	5992
Residues n_residues	374
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

▼

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

Maximum dimension Dmax dmax	72.4 Å
Rg (real space) rg_real	22.69 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.1170e+07
I(0) uncertainty (real space) i0_real_error	3.7070e+05
Rg (reciprocal space) rg_reciprocal	22.71 Å
I(0) (reciprocal space) i0_reciprocal	31170000.0000
Solution quality estimate total_estimate	0.8992
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.211
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2604000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.998

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6133

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	Darobactin
Molecular weight formula_weight	971.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

WNXSKSF

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7nrfA01
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	79.610 Å
Unit-cell length b length_b	79.814 Å
Unit-cell length c length_c	89.346 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	42.850 Å
R factor r_factor	0.2190
R_work r_work	0.2182
R_free r_free	0.2324

fit	/app/data/saxs_computation/nr/7nrf/7nrf.fit
pddf	/app/data/pr_computation/nr/7nrf/7nrf.pr.out
profile	/app/data/saxs_computation/nr/7nrf/7nrf.dat

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2)

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)