SAXSdb — 3nb3

▼

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

Outer membrane protein A

OrganismNot specified

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 × 240 PDB declaration: 240-MERIC（240） Consistent with protein copy count	Chain A； UniProt 1–346 Chain B； UniProt 1–346 Chain C； UniProt 1–346	Fragment：outer membrane protein A	Outer membrane protein C × 60 （P06996）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–346 Chain B； UniProt 1–346 Chain C； UniProt 1–346	Fragment：outer membrane protein A	Outer membrane protein C × 1 （P06996）	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
3	Protein heterocomplex Heteromer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain A； UniProt 1–346 Chain B； UniProt 1–346 Chain C； UniProt 1–346	Fragment：outer membrane protein A	Outer membrane protein C × 5 （P06996）	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
4	Protein heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 1–346 Chain B； UniProt 1–346 Chain C； UniProt 1–346	Fragment：outer membrane protein A	Outer membrane protein C × 6 （P06996）	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
5	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–346 Chain B； UniProt 1–346 Chain C； UniProt 1–346	Fragment：outer membrane protein A	Outer membrane protein C × 1 （P06996）	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

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 3NB3	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 method 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 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 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 mutation/modification Different oligomeric state 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
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 method 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 method 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 mutation/modification Different oligomeric state Different experimental method 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
9FZC Structure of OmpA-short in complex with nanobody Nb01 Deposited 2024-07-05	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 × 2 PDB declaration: dimeric	Chain A 22–191（170 aa）	Not recorded	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
9FZC Structure of OmpA-short in complex with nanobody Nb01 Deposited 2024-07-05	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 × 2 PDB declaration: dimeric	Chain B 22–191（170 aa）	Not recorded	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

7 other PDB entries and 9 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 1–346； UniProt 1–346 Author chain B； PDBConstruct 1–346； UniProt 1–346 Author chain C； PDBConstruct 1–346； UniProt 1–346

Outer membrane protein C

OrganismNot specified

UniProt P06996

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 × 240 PDB declaration: 240-MERIC（240） Consistent with protein copy count	Chain D； UniProt 22–367	Fragment：outer membrane protein C	Outer membrane protein A × 180 （P0A910）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 22–367	Fragment：outer membrane protein C	Outer membrane protein A × 3 （P0A910）	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
3	Protein heterocomplex Heteromer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain D； UniProt 22–367	Fragment：outer membrane protein C	Outer membrane protein A × 15 （P0A910）	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
4	Protein heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain D； UniProt 22–367	Fragment：outer membrane protein C	Outer membrane protein A × 18 （P0A910）	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
5	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 22–367	Fragment：outer membrane protein C	Outer membrane protein A × 3 （P0A910）	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

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 3NB3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2J1N osmoporin OmpC Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–367（346 aa） Chain B 22–367（346 aa） Chain C 22–367（346 aa）	Not recorded	MG MAGNESIUM ION × 3 CL CHLORIDE ION × 2 D12 DODECANE × 11	X-RAY DIFFRACTION X-ray crystallization conditions 25 MG/ML OMPC IN 25 MM TRIS-HCL (PH 8.0), 0.5 M NACL, 1.8 % (W/W) N-OCTYL-2- HYDROXYETHYLSULFOXIDE (C8HESO), 0.3 % (V/V) OCTYL-POLYOXYETHYLENE (OCTYL-POE) WERE EQUILIBRATED AGAINST A RESERVOIR SOLUTION CONTAINING 25 MM TRIS-HCL (PH 8.0), 0.5 M NACL AND 28% PEG2000.	Resolution 2.00 Å R-free 0.214
2J4U E.coli OmpC - camel Lactoferrin complex Deposited 2006-09-06	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 22–367（346 aa） Fragment：RESIDUES 22-367 Chain Q 22–367（346 aa） Fragment：RESIDUES 22-367 Chain R 22–367（346 aa） Fragment：RESIDUES 22-367	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.99 Å R-free 0.282
2J4U E.coli OmpC - camel Lactoferrin complex Deposited 2006-09-06	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain U 22–367（346 aa） Fragment：RESIDUES 22-367 Chain V 22–367（346 aa） Fragment：RESIDUES 22-367 Chain W 22–367（346 aa） Fragment：RESIDUES 22-367	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.99 Å R-free 0.282
2ZLE Cryo-EM structure of DegP12/OMP Deposited 2008-04-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain D 22–367（346 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；Embedded in vitreous ice using C-flat holey carbon grids (CF-2/2-4C-100, Protochip) and a Vitrobot (FEI) at 20 temperature and 100% relative humidity	Resolution 28.00 Å
4A8D DegP dodecamer with bound OMP Deposited 2011-11-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain M 22–367（346 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 300MM NACL, 50MM HEPES- NAOH；pH 8；300MM NACL, 50MM HEPES- NAOH cryo-EM vitrification conditions Cryogen ETHANE；EMBEDDED IN VITREOUS ICE USING C-FLAT HOLEY CARBON GRIDS AND A VITROBOT AT 20C.	Resolution 28.00 Å
8I8R Cryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs Deposited 2023-02-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–367（346 aa） Chain B 22–367（346 aa） Chain C 22–367（346 aa）	Not recorded	KDL (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris-buffered saline (TBS) buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
8I8X Cryo-EM Structure of OmpC3-MlaA-MlaC Complex in MSP2N2 Nanodiscs Deposited 2023-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 22–367（346 aa） Chain B 22–367（346 aa） Chain C 22–367（346 aa）	Not recorded	KDL (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris-buffered saline (TBS) buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å

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

View Construct and Data Evidence

UniProt name	OMPC_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–346； UniProt 22–367

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	3nb3
Deposition date deposition_date	2010-06-02
Structure title title	The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components
Keywords keywords	virus assembly, cementing protein, bacteriophage, Sf6, Shigella, beta-barrel, outer membrane protein, icosahedral, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	55.48 Å
Radius of gyration Rg (electron density) rg_electron	56.24 Å
Forward intensity I(0) i0	105410000.00
Molecular weight molecular_weight	83878.0 kDa
Excluded volume excluded_volume	104180 Å³
Envelope volume envelope_volume	183410 Å³
Hydration-shell volume shell_volume	29778 Å³
Envelope diameter envelope_diameter	184.8 Å
Shell Rg shell_rg	52.71 Å
Envelope Rg envelope_rg	54.14 Å
Shape Rg shape_rg	56.24 Å
Total Rg total_rg	56.12 Å
Total atoms total_atoms	5945
Residues n_residues	757
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	172.1 Å
Rg (real space) rg_real	55.95 Å
Rg uncertainty (real space) rg_real_error	2.20 Å
I(0) (real space) i0_real	1.0540e+08
I(0) uncertainty (real space) i0_real_error	2.4080e+06
Rg (reciprocal space) rg_reciprocal	55.03 Å
I(0) (reciprocal space) i0_reciprocal	105300000.0000
Solution quality estimate total_estimate	0.6333
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.868
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2257000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.294; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.347; Smooth: 0.001

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Outer membrane protein A
Molecular weight formula_weight	37272.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5945

MKKTAIAIAVALAGFATVAQAAPKDNTWYTGAKLGWSQYHDTGFINNNGPTHENKLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFGQGEAAPVVAPAPAPAPEVQTKHFTLKSDVLFNFNKATLKPEGQAALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSERRAQSVVDYLISKGIPADKISARGMGESNPVTGNTCDNVKQRAALIDCLAPDRRVEIEVKGIKDVVTQPQA

Entity 2 Entity 2 polymer

Description description	Outer membrane protein C
Molecular weight formula_weight	38336.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

AEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	19.00 Å
Resolution测定方法 resolution_method	model-based projection
颗粒数 num_particles	3232

fit	/app/data/saxs_computation/nb/3nb3/3nb3.fit
pddf	/app/data/pr_computation/nb/3nb3/3nb3.pr.out
profile	/app/data/saxs_computation/nb/3nb3/3nb3.dat

The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components

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

Outer membrane protein C

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)