4d9j

Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains

Method: X-RAY DIFFRACTION D_max: 223.3 Å Quality: GOOD

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

Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1

Influenza A virus

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 Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 3–164 Chain B； UniProt 3–164 Chain C； UniProt 3–164 Chain D； UniProt 3–164 Chain E； UniProt 3–164 Chain F； UniProt 3–164	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.92 Å R-free 0.294
2	Insufficient information Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain G； UniProt 3–164 Chain H； UniProt 3–164 Chain I； UniProt 3–164 Chain J； UniProt 3–164 Chain K； UniProt 3–164 Chain L； UniProt 3–164	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.92 Å R-free 0.294

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 4D9J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AA7 INFLUENZA VIRUS MATRIX PROTEIN CRYSTAL STRUCTURE AT PH 4.0 Deposited 1997-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–158（158 aa） Chain B 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；20% PEG 3350, 50MM NAH2PO4, PH 4.0	Resolution 2.08 Å R-free 0.280
1EA3 Influenza virus M1 protein Deposited 2000-11-03	Different construct 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 1–164（164 aa） Fragment：N-TERMINAL DOMAIN RESIDUES 1-164	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH7.5, 5% V/V ISOPROPANOL,6-10% PEG4000, pH 7.00	Resolution 2.30 Å R-free 0.313
1EA3 Influenza virus M1 protein Deposited 2000-11-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–164（164 aa） Fragment：N-TERMINAL DOMAIN RESIDUES 1-164	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH7.5, 5% V/V ISOPROPANOL,6-10% PEG4000, pH 7.00	Resolution 2.30 Å R-free 0.313
1HHI THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2 Deposited 1993-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 58–66（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1HHI THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2 Deposited 1993-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 58–66（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
3VDX Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains Deposited 2012-01-06	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Chain B 3–164（162 aa） Chain C 3–164（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.00 Å R-free 0.281
4IQ4 Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P21212 form Deposited 2013-01-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–165（163 aa） Chain B 3–165（163 aa） Chain C 3–165（163 aa） Chain D 3–165（163 aa） Chain E 3–165（163 aa） Chain F 3–165（163 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3,000, vapor diffusion, hanging drop, temperature 298K	Resolution 3.50 Å R-free 0.231
4ITV Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P212121 form Deposited 2013-01-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Chain B 3–164（162 aa） Chain C 3–164（162 aa） Chain D 3–164（162 aa） Chain E 3–164（162 aa） Chain F 3–164（162 aa） Chain G 3–164（162 aa） Chain H 3–164（162 aa） Chain I 3–164（162 aa） Chain J 3–164（162 aa） Chain K 3–164（162 aa） Chain L 3–164（162 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K	Resolution 3.60 Å R-free 0.240
4IVJ Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, I222 form Deposited 2013-01-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–165（163 aa） Chain B 3–165（163 aa） Chain C 3–165（163 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K	Resolution 7.35 Å R-free 0.288
4QES Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, I222 form Deposited 2014-05-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Fragment：SEE REMARK 999 Chain B 3–164（162 aa） Fragment：SEE REMARK 999 Chain C 3–164（162 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1 M sodium citrate, pH 4.4, 11% PEG3000, 200 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.19 Å R-free 0.295
4QF0 Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P21212 form Deposited 2014-05-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Fragment：SEE REMARK 999 Chain B 3–164（162 aa） Fragment：SEE REMARK 999 Chain C 3–164（162 aa） Fragment：SEE REMARK 999 Chain D 3–164（162 aa） Fragment：SEE REMARK 999 Chain E 3–164（162 aa） Fragment：SEE REMARK 999 Chain F 3–164（162 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Tris, pH 7.0, 10% PEG8000, 0.2 M magnesium chloride, 3% trehalose, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 6.49 Å R-free 0.324
4QFF Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P212121 form Deposited 2014-05-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Fragment：SEE REMARK 999 Chain B 3–164（162 aa） Fragment：SEE REMARK 999 Chain C 3–164（162 aa） Fragment：SEE REMARK 999 Chain D 3–164（162 aa） Fragment：SEE REMARK 999 Chain E 3–164（162 aa） Fragment：SEE REMARK 999 Chain F 3–164（162 aa） Fragment：SEE REMARK 999 Chain G 3–164（162 aa） Fragment：SEE REMARK 999 Chain H 3–164（162 aa） Fragment：SEE REMARK 999 Chain I 3–164（162 aa） Fragment：SEE REMARK 999 Chain J 3–164（162 aa） Fragment：SEE REMARK 999 Chain K 3–164（162 aa） Fragment：SEE REMARK 999 Chain L 3–164（162 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.1 M sodium/potassium phosphate, pH 5.8, 10% PEG8000, 0.2 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 7.81 Å R-free 0.339
5CQE 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1)) Deposited 2015-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa） Chain B 1–164（164 aa）	Not recorded	CL CHLORIDE ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；Protein: 12.8 mg/mL 10 mM Tris-HCl pH 8.3 500 mM NaCl 0.5 mM TCEP Crsytallization: The JCSG+ Suite (B9: 100 mM Citric acid pH 4.0 20% (w/v) PEG 6000; final pH 5.0 Cryocondition: Crystallization condition + sucrose (50%)	Resolution 2.10 Å R-free 0.197
5EUO PF6-M1-HLA-A2 Deposited 2015-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 58–66（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG3350, Imidazole	Resolution 2.10 Å R-free 0.281
5EUO PF6-M1-HLA-A2 Deposited 2015-11-18	Different construct 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 I 58–66（9 aa）	Not recorded	IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG3350, Imidazole	Resolution 2.10 Å R-free 0.281
6Z5L Helical reconstruction of influenza A virus M1 in complex with nucleic acid. Deposited 2020-05-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 80 PDB declaration: 80-meric	Chain A 1–252（252 aa）	Mutation：R134K	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 10 cryo-EM vitrification conditions Cryogen ETHANE；sample was applied 3 times each with 30s adsorption time	Resolution 3.80 Å

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	M1_I34A1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 287–448； UniProt 3–164 Author chain B； PDBConstruct 287–448； UniProt 3–164 Author chain C； PDBConstruct 287–448； UniProt 3–164 Author chain D； PDBConstruct 287–448； UniProt 3–164 Author chain E； PDBConstruct 287–448； UniProt 3–164 Author chain F； PDBConstruct 287–448； UniProt 3–164 Author chain G； PDBConstruct 287–448； UniProt 3–164 Author chain H； PDBConstruct 287–448； UniProt 3–164 Author chain I； PDBConstruct 287–448； UniProt 3–164 Author chain J； PDBConstruct 287–448； UniProt 3–164 Author chain K； PDBConstruct 287–448； UniProt 3–164 Author chain L； PDBConstruct 287–448； UniProt 3–164

Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1

Influenza A virus

UniProt P29715

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 Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–278 Chain B； UniProt 1–278 Chain C； UniProt 1–278 Chain D； UniProt 1–278 Chain E； UniProt 1–278 Chain F； UniProt 1–278	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.92 Å R-free 0.294
2	Insufficient information Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain G； UniProt 1–278 Chain H； UniProt 1–278 Chain I； UniProt 1–278 Chain J； UniProt 1–278 Chain K； UniProt 1–278 Chain L； UniProt 1–278	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.92 Å R-free 0.294

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4D9J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BRO BROMOPEROXIDASE A2 Deposited 1996-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–277（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；1.8 M AMMONIUM SULFATE PH 8.0.	Resolution 2.05 Å
1BRO BROMOPEROXIDASE A2 Deposited 1996-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 1–277（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；1.8 M AMMONIUM SULFATE PH 8.0.	Resolution 2.05 Å
1BRT BROMOPEROXIDASE A2 MUTANT M99T Deposited 1998-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–277（277 aa）	Mutation：M99T	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；1.8 M AMMONIUM SULFATE 0.1 M TRIS/HCL, PH 8.5.	Resolution 1.50 Å R-free 0.164
3VDX Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains Deposited 2012-01-06	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–278（278 aa） Chain B 1–278（278 aa） Chain C 1–278（278 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.00 Å R-free 0.281
4IQ4 Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P21212 form Deposited 2013-01-10	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–278（278 aa） Chain B 1–278（278 aa） Chain C 1–278（278 aa） Chain D 1–278（278 aa） Chain E 1–278（278 aa） Chain F 1–278（278 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3,000, vapor diffusion, hanging drop, temperature 298K	Resolution 3.50 Å R-free 0.231
4ITV Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P212121 form Deposited 2013-01-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–278（278 aa） Chain B 1–278（278 aa） Chain C 1–278（278 aa） Chain D 1–278（278 aa） Chain E 1–278（278 aa） Chain F 1–278（278 aa） Chain G 1–278（278 aa） Chain H 1–278（278 aa） Chain I 1–278（278 aa） Chain J 1–278（278 aa） Chain K 1–278（278 aa） Chain L 1–278（278 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K	Resolution 3.60 Å R-free 0.240
4IVJ Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, I222 form Deposited 2013-01-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–278（278 aa） Chain B 1–278（278 aa） Chain C 1–278（278 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K	Resolution 7.35 Å R-free 0.288
4QES Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, I222 form Deposited 2014-05-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–278（278 aa） Fragment：SEE REMARK 999 Chain B 1–278（278 aa） Fragment：SEE REMARK 999 Chain C 1–278（278 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1 M sodium citrate, pH 4.4, 11% PEG3000, 200 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.19 Å R-free 0.295
4QF0 Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P21212 form Deposited 2014-05-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–278（278 aa） Fragment：SEE REMARK 999 Chain B 1–278（278 aa） Fragment：SEE REMARK 999 Chain C 1–278（278 aa） Fragment：SEE REMARK 999 Chain D 1–278（278 aa） Fragment：SEE REMARK 999 Chain E 1–278（278 aa） Fragment：SEE REMARK 999 Chain F 1–278（278 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Tris, pH 7.0, 10% PEG8000, 0.2 M magnesium chloride, 3% trehalose, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 6.49 Å R-free 0.324
4QFF Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P212121 form Deposited 2014-05-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–278（278 aa） Fragment：SEE REMARK 999 Chain B 1–278（278 aa） Fragment：SEE REMARK 999 Chain C 1–278（278 aa） Fragment：SEE REMARK 999 Chain D 1–278（278 aa） Fragment：SEE REMARK 999 Chain E 1–278（278 aa） Fragment：SEE REMARK 999 Chain F 1–278（278 aa） Fragment：SEE REMARK 999 Chain G 1–278（278 aa） Fragment：SEE REMARK 999 Chain H 1–278（278 aa） Fragment：SEE REMARK 999 Chain I 1–278（278 aa） Fragment：SEE REMARK 999 Chain J 1–278（278 aa） Fragment：SEE REMARK 999 Chain K 1–278（278 aa） Fragment：SEE REMARK 999 Chain L 1–278（278 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.1 M sodium/potassium phosphate, pH 5.8, 10% PEG8000, 0.2 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 7.81 Å R-free 0.339

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

View Construct and Data Evidence

UniProt name	BPOA2_STRAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–278； UniProt 1–278 Author chain B； PDBConstruct 1–278； UniProt 1–278 Author chain C； PDBConstruct 1–278； UniProt 1–278 Author chain D； PDBConstruct 1–278； UniProt 1–278 Author chain E； PDBConstruct 1–278； UniProt 1–278 Author chain F； PDBConstruct 1–278； UniProt 1–278 Author chain G； PDBConstruct 1–278； UniProt 1–278 Author chain H； PDBConstruct 1–278； UniProt 1–278 Author chain I； PDBConstruct 1–278； UniProt 1–278 Author chain J； PDBConstruct 1–278； UniProt 1–278 Author chain K； PDBConstruct 1–278； UniProt 1–278 Author chain L； PDBConstruct 1–278； UniProt 1–278

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4d9j
Deposition date deposition_date	2012-01-11
Structure title title	Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains
Keywords keywords	protein design, bionanotechnology, protein assembly, symmetry, biomaterials, DE NOVO PROTEIN; DE NOVO 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	73.53 Å
Radius of gyration Rg (electron density) rg_electron	74.03 Å
Forward intensity I(0) i0	4451870000.00
Molecular weight molecular_weight	574190.0 kDa
Excluded volume excluded_volume	721940 Å³
Envelope volume envelope_volume	1115700 Å³
Hydration-shell volume shell_volume	132190 Å³
Envelope diameter envelope_diameter	261.2 Å
Shell Rg shell_rg	65.26 Å
Envelope Rg envelope_rg	72.49 Å
Shape Rg shape_rg	74.01 Å
Total Rg total_rg	73.94 Å
Total atoms total_atoms	40596
Residues n_residues	5256
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	223.3 Å
Rg (real space) rg_real	73.51 Å
Rg uncertainty (real space) rg_real_error	1.53 Å
I(0) (real space) i0_real	4.4430e+09
I(0) uncertainty (real space) i0_real_error	9.6720e+07
Rg (reciprocal space) rg_reciprocal	72.29 Å
I(0) (reciprocal space) i0_reciprocal	4438000000.0000
Solution quality estimate total_estimate	0.8384
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	85.1 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	-0.368
Angular range angular_range	— – 0.1050 Å⁻¹
Current regularization parameter α current_alpha	0.0111
Highest regularization parameter α highest_alpha	200000000.0000
Real-space data points n_real_points	22
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.020

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

Domain ID domain_id	4d9jA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jE03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jF03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jG03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jH03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jI02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jI03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jJ02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jJ03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jK02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jK03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

Domain ID domain_id	4d9jL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4d9jL02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	4d9jL03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

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8. Citations (1)

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Unit-cell length a length_a	122.700 Å
Unit-cell length b length_b	187.410 Å
Unit-cell length c length_c	283.390 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	48

Space group space_group	P 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	3.920 Å
Low-resolution limit resolution_low	19.893 Å
R factor r_factor	0.2828
R_work r_work	0.2822
R_free r_free	0.2936

Description description	Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
Molecular weight formula_weight	50264.4 kDa
EC 编号 ec_number	1.11.1.-
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	40596

Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains

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

Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Influenza A virus
NCBI Class编号 ncbi_taxonomy_id	211044
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/d9/4d9j/4d9j.fit
pddf	/app/data/pr_computation/d9/4d9j/4d9j.pr.out
profile	/app/data/saxs_computation/d9/4d9j/4d9j.dat