SAXSdb — 9fzc

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

Outer membrane protein A

Escherichia coli K-12

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 22–191	Not recorded	Nanobody 01 × 1 OCT N-OCTANE × 6 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M sodium acetate pH 5.5, 0.2 M calcium acetate, 25 % PEG MME 2K	Resolution 2.27 Å R-free 0.234
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 22–191	Not recorded	Nanobody 01 × 1 OCT N-OCTANE × 11 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M sodium acetate pH 5.5, 0.2 M calcium acetate, 25 % PEG MME 2K	Resolution 2.27 Å R-free 0.234

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 9FZC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BXW OUTER MEMBRANE PROTEIN A (OMPA) TRANSMEMBRANE DOMAIN Deposited 1998-10-03	Different construct Different mutation/modification 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 21–192（172 aa） Fragment：TRANSMEMBRANE DOMAIN	Mutation：F23L, Q34K, K107Y	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；10 % PEG-8000 10 % MPD 0.05 M POTASSIUM PHOSPHATE PH 5.0	Resolution 2.50 Å R-free 0.235
1G90 NMR Solution Structure of Outer Membrane Protein A Transmembrane Domain: 10 conformers Deposited 2000-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–197（176 aa） Fragment：TRANSMEMBRANE DOMAIN, RESIDUES 1-176	Mutation：W15F, W57F, W102F, W103F.	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；323 K；Ionic strength (raw mmCIF value) 0.050；Pressure ambient NMR sample composition 1mM OmpA(0-176) U-15N,13C,2H; 600 mM D38-DPC; 10 mM phosphate buffer; pH 6.3; 50 mM NaCl \| 95% H2O/5% D2O	Resolution not provided
2GE4 High-resolution solution structure of outer membrane protein A transmembrane domain Deposited 2006-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–197（176 aa） Fragment：transmembrane domain	Mutation：W15F, W57F, W102F, W143F	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；223 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition 1mM OmpA U-2H,13C,15N; 500mM DPC; 10mM phosphate buffer; pH 6.3; 50mM NaCl \| 90% H2O/10% D2O	Resolution not provided
2JMM NMR solution structure of a minimal transmembrane beta-barrel platform protein Deposited 2006-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–197（155 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N; 80% 2H] BBP+EF, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3NB3 The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components Deposited 2010-06-02	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 × 240 PDB declaration: 240-MERIC	Chain A 1–346（346 aa） Fragment：outer membrane protein A Chain B 1–346（346 aa） Fragment：outer membrane protein A Chain C 1–346（346 aa） Fragment：outer membrane protein A	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2；pH 7.4；10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen.	Resolution 19.00 Å
3NB3 The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components Deposited 2010-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–346（346 aa） Fragment：outer membrane protein A Chain B 1–346（346 aa） Fragment：outer membrane protein A Chain C 1–346（346 aa） Fragment：outer membrane protein A	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2；pH 7.4；10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen.	Resolution 19.00 Å
3NB3 The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components Deposited 2010-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 1–346（346 aa） Fragment：outer membrane protein A Chain B 1–346（346 aa） Fragment：outer membrane protein A Chain C 1–346（346 aa） Fragment：outer membrane protein A	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2；pH 7.4；10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen.	Resolution 19.00 Å
3NB3 The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components Deposited 2010-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–346（346 aa） Fragment：outer membrane protein A Chain B 1–346（346 aa） Fragment：outer membrane protein A Chain C 1–346（346 aa） Fragment：outer membrane protein A	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2；pH 7.4；10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen.	Resolution 19.00 Å
3NB3 The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components Deposited 2010-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–346（346 aa） Fragment：outer membrane protein A Chain B 1–346（346 aa） Fragment：outer membrane protein A Chain C 1–346（346 aa） Fragment：outer membrane protein A	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2；pH 7.4；10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen.	Resolution 19.00 Å
5M2Q Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–22（22 aa）	Mutation：W66F	CBY COB(II)INAMIDE × 1 CYN CYANIDE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG3350 HEPES pH 7 Tryptone	Resolution 1.70 Å R-free 0.249
5M2Q Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–22（22 aa）	Mutation：W66F	CBY COB(II)INAMIDE × 1 CYN CYANIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG3350 HEPES pH 7 Tryptone	Resolution 1.70 Å R-free 0.249
6LYR Structure of the BAM complex Deposited 2020-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain P 180–188（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；27-30% PEG 400, 100mM NaCl	Resolution 3.28 Å R-free 0.280

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OMPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–172； UniProt 22–191 Author chain B； PDBConstruct 3–172； UniProt 22–191

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	9fzc
Deposition date deposition_date	2024-07-05
Structure title title	Structure of OmpA-short in complex with nanobody Nb01
Keywords keywords	Porin, Nanobody, Complex, 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	33.59 Å
Radius of gyration Rg (electron density) rg_electron	33.07 Å
Forward intensity I(0) i0	65101700.00
Molecular weight molecular_weight	65513.0 kDa
Excluded volume excluded_volume	82523 Å³
Envelope volume envelope_volume	109760 Å³
Hydration-shell volume shell_volume	28361 Å³
Envelope diameter envelope_diameter	106.9 Å
Shell Rg shell_rg	38.93 Å
Envelope Rg envelope_rg	32.40 Å
Shape Rg shape_rg	33.06 Å
Total Rg total_rg	33.57 Å
Total atoms total_atoms	9190
Residues n_residues	578
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	104.2 Å
Rg (real space) rg_real	33.57 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	6.5100e+07
I(0) uncertainty (real space) i0_real_error	1.0020e+06
Rg (reciprocal space) rg_reciprocal	33.59 Å
I(0) (reciprocal space) i0_reciprocal	65100000.0000
Solution quality estimate total_estimate	0.8800
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.5 Å
Skewness Skewness skewness	0.107
Kurtosis Kurtosis kurtosis	-0.710
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2197000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.761

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Outer membrane protein A
Molecular weight formula_weight	18993.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9466

MSAPKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFA

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Nanobody 01
Molecular weight formula_weight	13458.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPSQVQLVESGGGLVQPGGSLRLSCVVSGTGFTFSKSPMSWARQAPGKEREWVSAIFADSSTYYSDSVRGRFTISRDNAKNTVYLQMNNVKPEDTAVYYCGHRRLGKTTYDYRGKGTRVTVSA

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli K-12

Entity 3 Entity 3 non-polymer

Description description	N-OCTANE
Molecular weight formula_weight	114.2 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	276

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8. Citations (1)

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Unit-cell length a length_a	56.048 Å
Unit-cell length b length_b	55.296 Å
Unit-cell length c length_c	107.805 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.270 Å
Low-resolution limit resolution_low	107.790 Å
R factor r_factor	0.2090
R_work r_work	0.2076
R_free r_free	0.2344

fit	/app/data/saxs_computation/fz/9fzc/9fzc.fit
pddf	/app/data/pr_computation/fz/9fzc/9fzc.pr.out
profile	/app/data/saxs_computation/fz/9fzc/9fzc.dat

Structure of OmpA-short in complex with nanobody Nb01

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

Outer membrane protein A

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

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)