6p8k

Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX

Method: X-RAY DIFFRACTION D_max: 136.4 Å Quality: GOOD

▼

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

Bacterioferritin

Escherichia coli K-12

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 1–158 Chain B； UniProt 1–158 Chain C； UniProt 1–158 Chain D； UniProt 1–158 Chain E； UniProt 1–158 Chain F； UniProt 1–158 Chain G； UniProt 1–158 Chain H； UniProt 1–158 Chain I； UniProt 1–158 Chain J； UniProt 1–158 Chain K； UniProt 1–158 Chain L； UniProt 1–158	Not recorded	ZN ZINC ION × 24 ZNH PROTOPORPHYRIN IX CONTAINING ZN × 12 NA SODIUM ION × 8 MLI MALONATE ION × 56	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；2.4 M sodium malonate, pH 6.0	Resolution 1.70 Å R-free 0.217

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 6P8K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCF THE STRUCTURE OF A UNIQUE, TWO-FOLD SYMMETRIC, HAEM-BINDING SITE Deposited 1993-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	MN MANGANESE (II) ION × 48 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1BFR IRON STORAGE AND ELECTRON TRANSPORT Deposited 1994-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa） Chain M 1–158（158 aa） Chain N 1–158（158 aa） Chain O 1–158（158 aa） Chain P 1–158（158 aa） Chain Q 1–158（158 aa） Chain R 1–158（158 aa） Chain S 1–158（158 aa） Chain T 1–158（158 aa） Chain U 1–158（158 aa） Chain V 1–158（158 aa） Chain W 1–158（158 aa） Chain X 1–158（158 aa）	Not recorded	MN MANGANESE (II) ION × 48 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions THIS MONOCLINIC CRYSTAL WAS GROWN FROM A SOLUTION OF THE PROTEIN IN DISTILLED WATER BY THE ADDITION OF MN*CL2.	Resolution 2.94 Å
2HTN E. coli bacterioferritin in its as-isolated form Deposited 2006-07-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa）	Not recorded	FE FE (III) ION × 48 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% (v/v) PEG400, 0.2M MGCl2, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.188
2VXI The binding of heme and zinc in Escherichia coli Bacterioferritin Deposited 2008-07-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 24 ZN ZINC ION × 48 SO4 SULFATE ION × 58	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；60% AMSO4, 20MM TRIS-HCL PH7.5, 0.1M NACL	Resolution 1.91 Å R-free 0.216
2Y3Q 1.55A structure of apo bacterioferritin from E. coli Deposited 2010-12-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 24 SO4 SULFATE ION × 38 ACT ACETATE ION × 24 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；1.8M AMMONIUM SULPHATE, 100MM ACETATE, PH 5.5	Resolution 1.55 Å R-free 0.200
3E1J Crystal structure of E. coli Bacterioferritin (BFR) with an unoccupied ferroxidase centre (APO-BFR). Deposited 2008-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 32 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. CRYSTALS LATER SOAKED IN CRYOPROTECTANT AT PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, pH 5.00	Resolution 2.70 Å R-free 0.263
3E1L Crystal structure of E. coli Bacterioferritin (BFR) soaked in phosphate with an alternative conformation of the unoccupied Ferroxidase centre (APO-BFR II). Deposited 2008-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 32 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；1.8 M AMMOMIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. SUBSEQUENTLY, THE CRYSTALS WERE SOAKED IN A CRYO-PROTECTANT BUFFER CONTAINING PHOSPHATE BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00	Resolution 2.50 Å R-free 0.248
3E1M Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR) Deposited 2008-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 32 FE2 FE (II) ION × 72 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. SUBSEQUENTLY, APO-BFR CRYSTALS WERE SOAKED IN A CRYOPROTECTANCT CONTAINING FE2+ AND BUFFERED USING MOPS PH 7 IN PLACE OF CITRATE PH 5. EXPOSURE TO IRON WAS LIMITED TO 2.5 MINUTES BEFORE FLASH FREEZING IN LIQUID NITROGEN. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00	Resolution 2.70 Å R-free 0.259
3E1N Crystal structure of E. coli Bacterioferritin (BFR) after a 65 minute (aerobic) exposure to FE(II) revealing a possible MU-OXO bridge/MU-Hydroxy bridged DIIRON intermediate at the ferroxidase centre. (FE(III)-O-FE(III)-BFR). Deposited 2008-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 32 FE2 FE (II) ION × 48 UNL UNKNOWN LIGAND × 24 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. CRYSTALS OF OF APO-BFR WERE SUBSEQUENTLY SOAKED AEROBICALLY FOR 65 MINUTES IN A SOLUTION CONTAINING FE2+ AND BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE PH 5. AFTER 65MIN EXPOSURE TO IRON AND AIR, THE CRYSTAL WAS FLASH FROZEN IN LIQUID NITROGEN AND X-RAY DIFFRACTION DATA COLLECTED. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00	Resolution 2.80 Å R-free 0.268
3E1O Crystal structure of E. coli Bacterioferritin (BFR) with two ZN(II) ION sites at the Ferroxidase centre (ZN-BFR). Deposited 2008-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 32 ZN ZINC ION × 48 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；APO-BFR CRYSTALIZED IN 1.8 M AMMONIUM SULFATE, 0.1 M TRI-SODIUM CITRATE PH 5.0. CRYSTAL WAS THEN SOAKED IN A CRYOPROTECTANT CONTAINING ZN2+ IONS AND BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE. PLEASE SEE PAPER FO FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00	Resolution 2.95 Å R-free 0.252
3E1P Crystal structure of E. coli Bacterioferritin (BFR) in which the Ferroxidase centre is inhibited with ZN(II) and high occupancy iron is bound within the cavity. Deposited 2008-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 32 ZN ZINC ION × 48 FE2 FE (II) ION × 24 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5. APO-BFR CRYSTALS WERE SUBSEQUENTLY (AEROBICALLY) SOAKED IN A CRYOPROTECTANT SOLUTION CONTAINING FE2+ (AND BUFFERED AT PH 7.0 WITH 0.1 M MOPS IN PLACE OF CITRATE) FOR 65 MINUTES BEFORE FALSH FREEZING AND DATA COLLECTION. PLEASE SEE PAPER FOR FULL DETAILS., PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00	Resolution 2.40 Å R-free 0.260
3E1Q Crystal structure of W133F variant E. coli Bacterioferritn with iron. Deposited 2008-08-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F Mutation：W133F	SO4 SULFATE ION × 32 FE2 FE (II) ION × 48 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；BFR PROTEIN WAS PRE-LOADED WITH IRON AND THEN CRYSTALLIZED OVERNIGHT IN 1.8 M AMMONIUM SULFATE, 0.1 M MES PH 5.8. PLEASE SEE THE ORIGINAL PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.80	Resolution 2.60 Å R-free 0.263
3E2C Escherichia coli Bacterioferritin Mutant E128R/E135R Deposited 2008-08-05	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 1–158（158 aa） Chain B 1–158（158 aa）	Mutation：E128R, E135R Mutation：E128R, E135R	ZN ZINC ION × 2 SO4 SULFATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；303.15 K；20% PEG 4000, 0.2M Li2SO4, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 303.15K	Resolution 1.80 Å R-free 0.228
3GHQ Crystal Structure of E. coli W35F BFR mutant Deposited 2009-03-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F Mutation：W35F	SO4 SULFATE ION × 42 FE FE (III) ION × 24 HEM PROTOPORPHYRIN IX CONTAINING FE × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；289 K；2.45M Ammonium Sulfate, 0.1M sodium Citrate pH 5.0, temperature 289K	Resolution 2.70 Å R-free 0.262
4CVR Structure of Apobacterioferritin Y25F variant Deposited 2014-03-29	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 1–158（158 aa）	Mutation：YES	ZN ZINC ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.10 Å R-free 0.165
4CVS Structure of Apobacterioferritin Y45F variant Deposited 2014-03-29	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 1–158（158 aa）	Mutation：YES	CD CADMIUM ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.39 Å R-free 0.225
4CVT Structure of Apobacterioferritin Y58F variant Deposited 2014-03-29	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 1–158（158 aa）	Mutation：YES	ZN ZINC ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.79 Å R-free 0.214
4XKS E. coli BFR variant Y45F Deposited 2015-01-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-mer	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F Mutation：Y45F	SO4 SULFATE ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；1.6M Ammonium Sulfate, 0.1M sodium citrate	Resolution 1.57 Å R-free 0.172
4XKU E coli BFR variant Y114F Deposited 2015-01-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F Mutation：Y114F	SO4 SULFATE ION × 30	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；1.6M ammonium sulfate 0.1M sodium citrate	Resolution 1.78 Å R-free 0.217
5XGO The Ferritin E-Domain: Toward Understanding Its Role in Protein Cage Assembly Through the Crystal Structure of a Maxi-/Mini-Ferritin Chimera Deposited 2017-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 138–158（21 aa） Chain B 138–158（21 aa） Chain C 138–158（21 aa） Chain D 138–158（21 aa） Chain E 138–158（21 aa） Chain F 138–158（21 aa） Chain G 138–158（21 aa） Chain H 138–158（21 aa） Chain I 138–158（21 aa） Chain J 138–158（21 aa） Chain K 138–158（21 aa） Chain L 138–158（21 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；292.15 K；0.2M lithium sulphate, 18% PEG 1000, pH 4.2	Resolution 1.99 Å R-free 0.207
6P8L Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-ray Data) Deposited 2019-06-07	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa） Chain K 1–158（158 aa） Chain L 1–158（158 aa）	Not recorded	ZN ZINC ION × 24 NA SODIUM ION × 8 MLI MALONATE ION × 56 ZNH PROTOPORPHYRIN IX CONTAINING ZN × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；2.4 M sodium malonate, pH 6.0	Resolution 2.10 Å R-free 0.240

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BFR_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158 Author chain B； PDBConstruct 1–158； UniProt 1–158 Author chain C； PDBConstruct 1–158； UniProt 1–158 Author chain D； PDBConstruct 1–158； UniProt 1–158 Author chain E； PDBConstruct 1–158； UniProt 1–158 Author chain F； PDBConstruct 1–158； UniProt 1–158 Author chain G； PDBConstruct 1–158； UniProt 1–158 Author chain H； PDBConstruct 1–158； UniProt 1–158 Author chain I； PDBConstruct 1–158； UniProt 1–158 Author chain J； PDBConstruct 1–158； UniProt 1–158 Author chain K； PDBConstruct 1–158； UniProt 1–158 Author chain L； PDBConstruct 1–158； UniProt 1–158

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6p8k
Deposition date deposition_date	2019-06-07
Structure title title	Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX
Keywords keywords	bacterioferritin, zinc protoporphyrin IX, photosensitizer, ferritin, metal binding protein, oxidoreductase; METAL BINDING PROTEIN, OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	46.59 Å
Radius of gyration Rg (electron density) rg_electron	46.16 Å
Forward intensity I(0) i0	785288000.00
Molecular weight molecular_weight	228370.0 kDa
Excluded volume excluded_volume	283850 Å³
Envelope volume envelope_volume	422590 Å³
Hydration-shell volume shell_volume	75339 Å³
Envelope diameter envelope_diameter	132.7 Å
Shell Rg shell_rg	53.46 Å
Envelope Rg envelope_rg	43.36 Å
Shape Rg shape_rg	46.15 Å
Total Rg total_rg	46.50 Å
Total atoms total_atoms	15998
Residues n_residues	1884
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	136.4 Å
Rg (real space) rg_real	46.32 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	7.8530e+08
I(0) uncertainty (real space) i0_real_error	1.4230e+07
Rg (reciprocal space) rg_reciprocal	46.59 Å
I(0) (reciprocal space) i0_reciprocal	785500000.0000
Solution quality estimate total_estimate	0.8954
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	60.2 Å
Skewness Skewness skewness	-0.042
Kurtosis Kurtosis kurtosis	-0.868
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28870000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.720

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Bacterioferritin
Molecular weight formula_weight	18518.0 kDa
EC 编号 ec_number	1.16.3.1
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

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	19097

MKGDTKVINYLNKLLGNELVAINQYFLHARMFKNWGLKRLNDVEYHESIDEMKHADRYIERILFLEGLPNLQDLGKLNIGEDVEEMLRSDLALELDGAKNLREAIGYADSVHDYVSRDMMIEILRDEEGHIDWLETELDLIQKMGLQNYLQAQIREEG

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING ZN
Molecular weight formula_weight	626.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2530

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6p8ka_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kb_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kc_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kd_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8ke_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kf_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kg_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kh_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8ki_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kj_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kk_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d6p8kl_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

CATH v4.4 (12 domains)

Domain ID domain_id	6p8kA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	6p8kL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

▶

8. Citations (1)

▶

Unit-cell length a length_a	207.852 Å
Unit-cell length b length_b	207.852 Å
Unit-cell length c length_c	142.657 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	96

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	tetragonal

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.1916
R_work r_work	0.1915
R_free r_free	0.2175

fit	/app/data/saxs_computation/p8/6p8k/6p8k.fit
pddf	/app/data/pr_computation/p8/6p8k/6p8k.pr.out
profile	/app/data/saxs_computation/p8/6p8k/6p8k.dat