SAXSdb — 5m2q

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

Outer membrane protein A,Vitamin B12-binding protein

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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–22	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
2	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–22	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

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 5M2Q	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 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 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
6LYR Structure of the BAM complex Deposited 2020-02-15	Different construct Different mutation/modification 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
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 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 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 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 1–22； UniProt 1–22 Author chain B； PDBConstruct 1–22； UniProt 1–22

Outer membrane protein A,Vitamin B12-binding protein

Escherichia coli

UniProt P37028

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 22–266	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
2	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 22–266	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

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 5M2Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N2Z 2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli Deposited 2002-10-24	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 22–266（245 aa）	Not recorded	CD CADMIUM ION × 13 CL CHLORIDE ION × 4 CNC CYANOCOBALAMIN × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.210
1N2Z 2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli Deposited 2002-10-24	Different mutation/modification 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 22–266（245 aa）	Not recorded	CD CADMIUM ION × 9 CL CHLORIDE ION × 2 CNC CYANOCOBALAMIN × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.210
1N2Z 2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli Deposited 2002-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–266（245 aa） Chain B 22–266（245 aa）	Not recorded	CD CADMIUM ION × 22 CL CHLORIDE ION × 6 CNC CYANOCOBALAMIN × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.210
1N2Z 2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli Deposited 2002-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–266（245 aa） Chain B 22–266（245 aa）	Not recorded	CD CADMIUM ION × 22 CL CHLORIDE ION × 6 CNC CYANOCOBALAMIN × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.210
1N4A The Ligand Bound Structure of E.coli BtuF, the Periplasmic Binding Protein for Vitamin B12 Deposited 2002-10-30	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 23–266（244 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CNC CYANOCOBALAMIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；NaCl, ethanol, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.261
1N4A The Ligand Bound Structure of E.coli BtuF, the Periplasmic Binding Protein for Vitamin B12 Deposited 2002-10-30	Different construct Different mutation/modification 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 23–266（244 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CNC CYANOCOBALAMIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；NaCl, ethanol, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.261
1N4D The Ligand-Free Structure of E coli BtuF, the Periplasmic Binding Protein for Vitamin B12 Deposited 2002-10-30	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 23–266（244 aa）	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 4.6；294 K；acetate, PEG4000, (NH4)OAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.298
1N4D The Ligand-Free Structure of E coli BtuF, the Periplasmic Binding Protein for Vitamin B12 Deposited 2002-10-30	Different construct Different mutation/modification 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 23–266（244 aa）	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 4.6；294 K；acetate, PEG4000, (NH4)OAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.298
2QI9 ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF Deposited 2007-07-03	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 F 22–266（245 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；30-38% (w/v) polyethylene glycol 400, 50mM either of Tris‑HCl pH 8.4 or Glycine-NaOH pH 9.4 and 400mM (NH4)2SO4., VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.280
4DBL Crystal structure of E159Q mutant of BtuCDF Deposited 2012-01-16	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 E 22–266（245 aa）	Not recorded	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；0.1M sodium citrate, pH 5.4, 0.3-0.4M ammonium sulphate, 30-35% PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.49 Å R-free 0.251
4DBL Crystal structure of E159Q mutant of BtuCDF Deposited 2012-01-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 22–266（245 aa）	Not recorded	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；0.1M sodium citrate, pH 5.4, 0.3-0.4M ammonium sulphate, 30-35% PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.49 Å R-free 0.251
4FI3 Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state Deposited 2012-06-07	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 F 22–266（245 aa） Fragment：UNP residues 22-266	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；20-30% PEG400, 100 mM ADA pH6.8, 100 mM Na/K-citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.47 Å R-free 0.274
5M29 Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-12	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–266（245 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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；HEPES sodium pH 7.0 PEG3350 Tryptone	Resolution 1.50 Å R-free 0.213
5M29 Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-12	Different mutation/modification 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 22–266（245 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CBY COB(II)INAMIDE × 1 CYN CYANIDE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；HEPES sodium pH 7.0 PEG3350 Tryptone	Resolution 1.50 Å R-free 0.213
5M34 Structure of cobinamide-bound BtuF mutant W66Y, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-14	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–266（245 aa）	Not recorded	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 1.60 Å R-free 0.233
5M34 Structure of cobinamide-bound BtuF mutant W66Y, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-14	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–266（245 aa）	Not recorded	CBY COB(II)INAMIDE × 1 CYN CYANIDE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG3350 HEPES pH 7 Tryptone	Resolution 1.60 Å R-free 0.233
5M3B Structure of cobinamide-bound BtuF mutant W66L, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-14	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–266（245 aa）	Not recorded	CYN CYANIDE ION × 2 CBY COB(II)INAMIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG3350 HEPES pH 7 Tryptone	Resolution 1.50 Å R-free 0.229
5M3B Structure of cobinamide-bound BtuF mutant W66L, the periplasmic vitamin B12 binding protein in E.coli Deposited 2016-10-14	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–266（245 aa）	Not recorded	CYN CYANIDE ION × 1 CBY COB(II)INAMIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG3350 HEPES pH 7 Tryptone	Resolution 1.50 Å R-free 0.229
5OVW Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli Deposited 2017-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 22–266（245 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG4000, Tris-HCl, Magnesium chloride	Resolution 2.65 Å R-free 0.259
5OVW Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli Deposited 2017-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–266（245 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG4000, Tris-HCl, Magnesium chloride	Resolution 2.65 Å R-free 0.259
5OVW Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli Deposited 2017-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 22–266（245 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG4000, Tris-HCl, Magnesium chloride	Resolution 2.65 Å R-free 0.259
5OVW Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli Deposited 2017-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 22–266（245 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG4000, Tris-HCl, Magnesium chloride	Resolution 2.65 Å R-free 0.259
5OVW Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli Deposited 2017-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 22–266（245 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG4000, Tris-HCl, Magnesium chloride	Resolution 2.65 Å R-free 0.259
5OVW Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli Deposited 2017-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 22–266（245 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；PEG4000, Tris-HCl, Magnesium chloride	Resolution 2.65 Å R-free 0.259

10 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BTUF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–269； UniProt 22–266 Author chain B； PDBConstruct 25–269； UniProt 22–266

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	5m2q
Deposition date deposition_date	2016-10-13
Structure title title	Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli
Keywords keywords	BtuF, Cobinamide, periplasmic binding protein, ABC transporter, Transport protein; 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	23.35 Å
Radius of gyration Rg (electron density) rg_electron	22.44 Å
Forward intensity I(0) i0	43379600.00
Molecular weight molecular_weight	52369.0 kDa
Excluded volume excluded_volume	66173 Å³
Envelope volume envelope_volume	76615 Å³
Hydration-shell volume shell_volume	27757 Å³
Envelope diameter envelope_diameter	76.3 Å
Shell Rg shell_rg	29.97 Å
Envelope Rg envelope_rg	22.63 Å
Shape Rg shape_rg	22.41 Å
Total Rg total_rg	23.40 Å
Total atoms total_atoms	3689
Residues n_residues	456
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	72.4 Å
Rg (real space) rg_real	23.20 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	4.3380e+07
I(0) uncertainty (real space) i0_real_error	5.0970e+05
Rg (reciprocal space) rg_reciprocal	23.24 Å
I(0) (reciprocal space) i0_reciprocal	43380000.0000
Solution quality estimate total_estimate	0.9036
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.0 Å
Skewness Skewness skewness	0.137
Kurtosis Kurtosis kurtosis	-0.481
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12060000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.996

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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,Vitamin B12-binding protein
Molecular weight formula_weight	31472.9 kDa
Mutation mutation	W66F
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	4085

MKKTAIAIAVALAGFATVAQAASMAAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTFQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCNALSQVDSGSLEVLFQGPGGSHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COB(II)INAMIDE
Molecular weight formula_weight	990.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	390

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5m2qa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.2 — TroA-like

Domain ID domain_id	d5m2qb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.2 — TroA-like

Domain ID domain_id	d5m2qb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	5m2qA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	5m2qA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	5m2qB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	5m2qB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

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8. Citations (1)

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Unit-cell length a length_a	136.560 Å
Unit-cell length b length_b	90.670 Å
Unit-cell length c length_c	50.810 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	19.710 Å
R factor r_factor	0.2109
R_work r_work	0.2089
R_free r_free	0.2492

fit	/app/data/saxs_computation/m2/5m2q/5m2q.fit
pddf	/app/data/pr_computation/m2/5m2q/5m2q.pr.out
profile	/app/data/saxs_computation/m2/5m2q/5m2q.dat

Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli

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

Outer membrane protein A,Vitamin B12-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Outer membrane protein A,Vitamin B12-binding protein

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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)