1dps

THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA

Method: X-RAY DIFFRACTION D_max: 100.5 Å Quality: GOOD

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

DPS

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	Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–166 Chain B； UniProt 1–166 Chain C； UniProt 1–166 Chain D； UniProt 1–166 Chain E； UniProt 1–166 Chain F； UniProt 1–166 Chain G； UniProt 1–166 Chain H； UniProt 1–166 Chain I； UniProt 1–166 Chain J； UniProt 1–166 Chain K； UniProt 1–166 Chain L； UniProt 1–166	Mutation：S164C	NA SODIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；1.55-1.7 M SODIUM FORMATE 13-16% PEG 8000 100 MM NACL 50 MM TRIS PH 8, pH 8.0	Resolution 1.60 Å R-free 0.220

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 1DPS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F30 THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN Deposited 2000-05-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 0–166（167 aa） Chain B 0–166（167 aa） Chain C 0–166（167 aa） Chain D 0–166（167 aa） Chain E 0–166（167 aa） Chain F 0–166（167 aa）	Not recorded	ZN ZINC ION × 12 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10mM MOPS, 100mM KCl, 10% glycerol + 100mM TrisHCL, 100mM KCl, 10% glycerol, 11% PEG 8000, and 5mM DTT, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.85 Å R-free 0.272
1F30 THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN Deposited 2000-05-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain G 0–166（167 aa） Chain H 0–166（167 aa） Chain I 0–166（167 aa） Chain J 0–166（167 aa） Chain K 0–166（167 aa） Chain L 0–166（167 aa）	Not recorded	ZN ZINC ION × 12 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10mM MOPS, 100mM KCl, 10% glycerol + 100mM TrisHCL, 100mM KCl, 10% glycerol, 11% PEG 8000, and 5mM DTT, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.85 Å R-free 0.272
1F33 THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN Deposited 2000-05-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 0–166（167 aa） Chain B 0–166（167 aa） Chain C 0–166（167 aa） Chain D 0–166（167 aa） Chain E 0–166（167 aa） Chain F 0–166（167 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10mM MOPS, 100mM KCl, 10% glycerol + 100mM TrisHCL, 100mM KCl, 10% glycerol, 11% PEG 8000, and 5mM DTT , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.244
1F33 THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN Deposited 2000-05-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain G 0–166（167 aa） Chain H 0–166（167 aa） Chain I 0–166（167 aa） Chain J 0–166（167 aa） Chain K 0–166（167 aa） Chain L 0–166（167 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10mM MOPS, 100mM KCl, 10% glycerol + 100mM TrisHCL, 100mM KCl, 10% glycerol, 11% PEG 8000, and 5mM DTT , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.244
1F33 THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN Deposited 2000-05-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 0–166（167 aa） Chain B 0–166（167 aa） Chain C 0–166（167 aa） Chain D 0–166（167 aa） Chain E 0–166（167 aa） Chain F 0–166（167 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10mM MOPS, 100mM KCl, 10% glycerol + 100mM TrisHCL, 100mM KCl, 10% glycerol, 11% PEG 8000, and 5mM DTT , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.244
1JRE DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN Deposited 2001-08-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 0–166（167 aa） Chain B 0–166（167 aa） Chain C 0–166（167 aa） Chain D 0–166（167 aa） Chain E 0–166（167 aa） Chain F 0–166（167 aa） Chain G 0–166（167 aa） Chain H 0–166（167 aa） Chain I 0–166（167 aa） Chain J 0–166（167 aa） Chain K 0–166（167 aa） Chain L 0–166（167 aa）	Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A	CD CADMIUM ION × 13 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10MM MOPS, 100MM KCL, 10% GLYCEROL + 100MM TRISHCL, 100MM KCL, 10% GLYCEROL, 11% PEG 8000, AND 5MM DTT, pH 8.10, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.264
1JTS DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN Deposited 2001-08-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 0–166（167 aa） Chain B 0–166（167 aa） Chain C 0–166（167 aa） Chain D 0–166（167 aa） Chain E 0–166（167 aa） Chain F 0–166（167 aa） Chain G 0–166（167 aa） Chain H 0–166（167 aa） Chain I 0–166（167 aa） Chain J 0–166（167 aa） Chain K 0–166（167 aa） Chain L 0–166（167 aa）	Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；10MM MOPS, 100MM KCL, 10% GLYCEROL + 100MM TRISHCL, 100MM KCL, 10% GLYCEROL, 11% PEG 8000, AND 5MM DTT, pH 8.10, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.268
1JTS DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN Deposited 2001-08-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain M 0–166（167 aa） Chain N 0–166（167 aa） Chain O 0–166（167 aa） Chain P 0–166（167 aa） Chain Q 0–166（167 aa） Chain R 0–166（167 aa） Chain S 0–166（167 aa） Chain T 0–166（167 aa） Chain U 0–166（167 aa） Chain V 0–166（167 aa） Chain W 0–166（167 aa） Chain X 0–166（167 aa）	Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；10MM MOPS, 100MM KCL, 10% GLYCEROL + 100MM TRISHCL, 100MM KCL, 10% GLYCEROL, 11% PEG 8000, AND 5MM DTT, pH 8.10, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.268
1L8H DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN Deposited 2002-03-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 0–166（167 aa） Chain B 0–166（167 aa） Chain C 0–166（167 aa） Chain D 0–166（167 aa） Chain E 0–166（167 aa） Chain F 0–166（167 aa） Chain G 0–166（167 aa） Chain H 0–166（167 aa） Chain I 0–166（167 aa） Chain J 0–166（167 aa） Chain K 0–166（167 aa） Chain L 0–166（167 aa）	Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A Mutation：D75C/D78A	K POTASSIUM ION × 12 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；10MM MOPS, 100MM KCL, 10%GLYCEROL + 100MM TRISHCL, 100MM KCL, 10% GLYCEROL, 11% PEG 8000, AND 5MM DTT, pH 8.10, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.20 Å R-free 0.250
1L8I Dna Protection and Binding by E. Coli DPS Protein Deposited 2002-03-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 0–166（167 aa） Chain B 0–166（167 aa） Chain C 0–166（167 aa） Chain D 0–166（167 aa） Chain E 0–166（167 aa） Chain F 0–166（167 aa） Chain G 0–166（167 aa） Chain H 0–166（167 aa） Chain I 0–166（167 aa） Chain J 0–166（167 aa） Chain K 0–166（167 aa） Chain L 0–166（167 aa）	Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A Mutation：D75C, D78A	K POTASSIUM ION × 12 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；10MM MOPS, 100MM KCL, 10%GLYCEROL + 100MM TRISHCL, 100MM KCL, 10% GLYCEROL, 11% PEG 8000, AND 5MM DTT, pH 8.10, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.00 Å R-free 0.250
2W9R Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS Deposited 2009-01-28	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 B 6–16（11 aa） Fragment：RESIDUES 10-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.70 Å R-free 0.254
3O2H E. coli ClpS in complex with a Leu N-end rule peptide Deposited 2010-07-22	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 B 6–16（11 aa） Fragment：unp residues 6-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；300 K；0.2 M Sodium Acetate, 0.1 M TRIS, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 1.70 Å R-free 0.224
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 mutation/modification 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 1–163（163 aa） Chain B 1–163（163 aa） Chain C 1–163（163 aa） Chain D 1–163（163 aa） Chain E 1–163（163 aa） Chain F 1–163（163 aa） Chain G 1–163（163 aa） Chain H 1–163（163 aa） Chain I 1–163（163 aa） Chain J 1–163（163 aa） Chain K 1–163（163 aa） Chain L 1–163（163 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
6GCM Escherichia coli DPS Deposited 2018-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 9–167（159 aa） Chain B 14–167（154 aa） Chain C 14–167（154 aa） Chain D 12–167（156 aa） Chain E 14–167（154 aa） Chain F 14–167（154 aa） Chain G 14–167（154 aa） Chain H 14–167（154 aa） Chain I 14–167（154 aa） Chain J 14–167（154 aa） Chain K 14–167（154 aa） Chain L 14–167（154 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION, RECRYSTALLIZATION；291 K；PEG 8000	Resolution 2.45 Å R-free 0.258
6GCM Escherichia coli DPS Deposited 2018-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain b 9–167（159 aa） Chain c 14–167（154 aa） Chain d 14–167（154 aa） Chain e 12–167（156 aa） Chain f 17–167（151 aa） Chain g 14–167（154 aa） Chain h 14–167（154 aa） Chain i 14–167（154 aa） Chain j 14–167（154 aa） Chain k 14–167（154 aa） Chain l 14–167（154 aa） Chain m 14–167（154 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION, RECRYSTALLIZATION；291 K；PEG 8000	Resolution 2.45 Å R-free 0.258
7AQS Crystal structure of E. coli DPS in space group P1 Deposited 2020-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–167（167 aa） Chain B 1–167（167 aa） Chain C 1–167（167 aa） Chain D 1–167（167 aa） Chain E 1–167（167 aa） Chain F 1–167（167 aa） Chain G 1–167（167 aa） Chain H 1–167（167 aa） Chain I 1–167（167 aa） Chain J 1–167（167 aa） Chain K 1–167（167 aa） Chain L 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	FE FE (III) ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.0, 6.73 % w/v PEG 5000 MME and 0.06 M KCl	Resolution 2.80 Å R-free 0.243
7AQS Crystal structure of E. coli DPS in space group P1 Deposited 2020-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain M 1–167（167 aa） Chain N 1–167（167 aa） Chain O 1–167（167 aa） Chain P 1–167（167 aa） Chain Q 1–167（167 aa） Chain R 1–167（167 aa） Chain S 1–167（167 aa） Chain T 1–167（167 aa） Chain U 1–167（167 aa） Chain V 1–167（167 aa） Chain W 1–167（167 aa） Chain X 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	FE FE (III) ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.0, 6.73 % w/v PEG 5000 MME and 0.06 M KCl	Resolution 2.80 Å R-free 0.243
8OUC Escherichia coli DPS Deposited 2023-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain AAA 1–167（167 aa） Chain BBB 1–167（167 aa） Chain CCC 1–167（167 aa） Chain DDD 1–167（167 aa） Chain EEE 1–167（167 aa） Chain FFF 1–167（167 aa） Chain GGG 1–167（167 aa） Chain HHH 1–167（167 aa） Chain III 1–167（167 aa） Chain JJJ 1–167（167 aa） Chain KKK 1–167（167 aa） Chain LLL 1–167（167 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；290 K；TRIS-HCl	Resolution 1.37 Å R-free 0.206
8PV9 Structure of DPS determined by cryoEM at 100 keV Deposited 2023-07-17	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 2–167（166 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9ZC2 Structure of E. Coli DNA protection during starvation protein (DPS) from single particle cryoEM Deposited 2025-11-22	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 1–167（167 aa） Chain B 1–167（167 aa） Chain C 1–167（167 aa） Chain D 1–167（167 aa） Chain E 1–167（167 aa） Chain F 1–167（167 aa） Chain G 1–167（167 aa） Chain H 1–167（167 aa） Chain I 1–167（167 aa） Chain J 1–167（167 aa） Chain K 1–167（167 aa） Chain L 1–167（167 aa）	Not recorded	FE FE (III) ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.30 Å

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPS_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–167； UniProt 1–166 Author chain B； PDBConstruct 2–167； UniProt 1–166 Author chain C； PDBConstruct 2–167； UniProt 1–166 Author chain D； PDBConstruct 2–167； UniProt 1–166 Author chain E； PDBConstruct 2–167； UniProt 1–166 Author chain F； PDBConstruct 2–167； UniProt 1–166 Author chain G； PDBConstruct 2–167； UniProt 1–166 Author chain H； PDBConstruct 2–167； UniProt 1–166 Author chain I； PDBConstruct 2–167； UniProt 1–166 Author chain J； PDBConstruct 2–167； UniProt 1–166 Author chain K； PDBConstruct 2–167； UniProt 1–166 Author chain L； PDBConstruct 2–167； UniProt 1–166

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	1dps
Deposition date deposition_date	1998-02-23
Structure title title	THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA
Keywords keywords	DNA-BINDING PROTEIN, FERRITIN, IRON SEQUESTRATION, STATIONARY PHASE, OXIDATIVE DAMAGE, DNA BINDING PROTEIN; DNA BINDING 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	36.53 Å
Radius of gyration Rg (electron density) rg_electron	35.45 Å
Forward intensity I(0) i0	663531000.00
Molecular weight molecular_weight	209060.0 kDa
Excluded volume excluded_volume	261820 Å³
Envelope volume envelope_volume	337470 Å³
Hydration-shell volume shell_volume	74984 Å³
Envelope diameter envelope_diameter	103.6 Å
Shell Rg shell_rg	45.62 Å
Envelope Rg envelope_rg	33.82 Å
Shape Rg shape_rg	35.42 Å
Total Rg total_rg	36.21 Å
Total atoms total_atoms	14710
Residues n_residues	1855
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	100.5 Å
Rg (real space) rg_real	36.11 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	6.6350e+08
I(0) uncertainty (real space) i0_real_error	8.1750e+06
Rg (reciprocal space) rg_reciprocal	36.37 Å
I(0) (reciprocal space) i0_reciprocal	663700000.0000
Solution quality estimate total_estimate	0.8937
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	-0.223
Kurtosis Kurtosis kurtosis	-0.641
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	2541000000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.959

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DPS
Molecular weight formula_weight	18736.4 kDa
Mutation mutation	S164C
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	16107

MSTAKLVKSKATNLLYTRNDVSDSEKKATVELLNRQVIQFIDLSLITKQAHWNMRGANFIAVHEMLDGFRTALIDHLDTMAERAVQLGGVALGTTQVINSKTPLKSYPLDIHNVQDHLKELADRYAIVANDVRKAIGEAKDDDTADILTAASRDLDKFLWFIECNIE

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1397

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1dpsa_
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	d1dpsb_
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	d1dpsc_
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	d1dpsd_
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	d1dpse_
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	d1dpsf_
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	d1dpsg_
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	d1dpsh_
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	d1dpsi_
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	d1dpsj_
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	d1dpsk_
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	d1dpsl_
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	1dpsA00
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	1dpsB00
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	1dpsC00
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	1dpsD00
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	1dpsE00
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	1dpsF00
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	1dpsG00
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	1dpsH00
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	1dpsI00
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	1dpsJ00
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	1dpsK00
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	1dpsL00
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

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8. Citations (1)

▶

Unit-cell length a length_a	134.410 Å
Unit-cell length b length_b	139.650 Å
Unit-cell length c length_c	118.110 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2200

fit	/app/data/saxs_computation/dp/1dps/1dps.fit
pddf	/app/data/pr_computation/dp/1dps/1dps.pr.out
profile	/app/data/saxs_computation/dp/1dps/1dps.dat