SAXSdb — 5hjf

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

Ferritin, Dps family protein

Nostoc punctiforme

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 1–182 Chain B； UniProt 1–182 Chain C； UniProt 1–182 Chain D； UniProt 1–182	Mutation：S2A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；25% SOKALAN HP 66, 0.1 M HEPES pH 7.0 and 0.2 M NaOAc	Resolution 1.59 Å R-free 0.146

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 5HJF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5HJH Dps4 from Nostoc punctiforme in complex with Fe ions Deposited 2016-01-13	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 5–182（178 aa） Chain B 5–182（178 aa） Chain C 5–182（178 aa） Chain D 5–182（178 aa）	Not recorded	FE FE (III) ION × 24 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；25% SOKALAN HP 66, 0.1 M HEPES pH 7.0 and 0.2 M NaOAc	Resolution 1.88 Å R-free 0.193
5I4J Dps4 from Nostoc punctiforme in complex with Zn ions Deposited 2016-02-12	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 6–182（177 aa） Chain B 6–182（177 aa） Chain C 6–182（177 aa） Chain D 6–182（177 aa）	Not recorded	ZN ZINC ION × 12 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% SOKALAN HP 66, 0.1M HEPES pH 7.0 and 0.2M NaOAc,	Resolution 2.39 Å R-free 0.214
7RZQ Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex Deposited 2021-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.09 Å
7RZR Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with D936Y mutation Deposited 2021-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Mutation：D936Y Mutation：D936Y Mutation：D936Y	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.27 Å
7RZS Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with L938F mutation Deposited 2021-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Mutation：L938F Mutation：L938F Mutation：L938F	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.52 Å
7RZT Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with S940F mutation Deposited 2021-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Mutation：S940F Mutation：S940F Mutation：S940F	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å
7RZU Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with A942S mutation Deposited 2021-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Mutation：A942S Mutation：A942S Mutation：A942S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
7RZV Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with V1176F mutation Deposited 2021-08-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.11 Å
7TIK Structure of the SARS-CoV-2 Omicron spike post-fusion bundle Deposited 2022-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 4–178（175 aa） Chain B 4–178（175 aa） Chain C 4–178（175 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
8CZI Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with extended HR2 Deposited 2022-05-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.22 Å
8FA1 Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with N969K mutation Deposited 2022-11-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 4–178（175 aa） Chain B 4–178（175 aa） Chain C 4–178（175 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.51 Å
8FA2 Cryo-EM structure of the SARS-CoV-2 Omicron HR1-42G complex Deposited 2022-11-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–178（174 aa） Chain B 5–178（174 aa） Chain C 5–178（174 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B2J981_NOSP7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–185； UniProt 1–182 Author chain B； PDBConstruct 4–185； UniProt 1–182 Author chain C； PDBConstruct 4–185； UniProt 1–182 Author chain D； PDBConstruct 4–185； UniProt 1–182

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5hjf
Deposition date deposition_date	2016-01-13
Structure title title	The apo form of Dps4 from Nostoc punctiforme
Keywords keywords	metal binding protein, ferredoxin, oxidative stress; METAL 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	31.22 Å
Radius of gyration Rg (electron density) rg_electron	30.45 Å
Forward intensity I(0) i0	105242000.00
Molecular weight molecular_weight	81484.0 kDa
Excluded volume excluded_volume	101760 Å³
Envelope volume envelope_volume	130550 Å³
Hydration-shell volume shell_volume	34911 Å³
Envelope diameter envelope_diameter	105.2 Å
Shell Rg shell_rg	38.36 Å
Envelope Rg envelope_rg	30.84 Å
Shape Rg shape_rg	30.40 Å
Total Rg total_rg	31.27 Å
Total atoms total_atoms	11283
Residues n_residues	722
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	98.3 Å
Rg (real space) rg_real	31.22 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.0520e+08
I(0) uncertainty (real space) i0_real_error	1.7620e+06
Rg (reciprocal space) rg_reciprocal	31.23 Å
I(0) (reciprocal space) i0_reciprocal	105200000.0000
Solution quality estimate total_estimate	0.9004
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.8 Å
Skewness Skewness skewness	0.280
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24760000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.872

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5hjfa_
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.25.1.0 — automated matches

Domain ID domain_id	d5hjfb_
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.25.1.0 — automated matches

Domain ID domain_id	d5hjfc_
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.25.1.0 — automated matches

Domain ID domain_id	d5hjfd1
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.25.1.0 — automated matches

Domain ID domain_id	d5hjfd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	5hjfA00
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	5hjfB00
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	5hjfC00
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	5hjfD00
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)

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Unit-cell length a length_a	101.884 Å
Unit-cell length b length_b	101.884 Å
Unit-cell length c length_c	146.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.590 Å
Low-resolution limit resolution_low	48.107 Å
R factor r_factor	0.1308
R_work r_work	0.1301
R_free r_free	0.1462

Description description	Ferritin, Dps family protein
Molecular weight formula_weight	20948.4 kDa
Mutation mutation	S2A
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12135

The apo form of Dps4 from Nostoc punctiforme

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

Ferritin, Dps family protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Nostoc punctiforme
NCBI Class编号 ncbi_taxonomy_id	272131
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	683

fit	/app/data/saxs_computation/hj/5hjf/5hjf.fit
pddf	/app/data/pr_computation/hj/5hjf/5hjf.pr.out
profile	/app/data/saxs_computation/hj/5hjf/5hjf.dat