SAXSdb — 21fy

▼

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

Cysteine desulfurase IscS

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–404 Chain B； UniProt 1–404	Non-standard monomer：Yes (specific site not provided by mmCIF)	PptA × 2 （A0A5Q2WBY0） SF4 IRON/SULFUR CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.85 Å

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 21FY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1P3W X-ray crystal structure of E. coli IscS Deposited 2003-04-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–404（404 aa） Chain B 1–404（404 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.1 K；PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22.1K	Resolution 2.10 Å R-free 0.236

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ISCS_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–404； UniProt 1–404 Author chain B； PDBConstruct 1–404； UniProt 1–404

PptA

Psychrobacter phage vB_PmaS_Y8A

UniProt A0A5Q2WBY0

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–250 Chain D； UniProt 1–250	Not recorded	Cysteine desulfurase IscS × 2 （P0A6B7） SF4 IRON/SULFUR CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.85 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A5Q2WBY0_9CAUD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 21–270； UniProt 1–250 Author chain D； PDBConstruct 21–270； UniProt 1–250

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	21fy
Deposition date deposition_date	2025-12-11
Structure title title	The cryo-EM structure of IscS-PptA complex
Keywords keywords	DNA phosphorothioation, anti-defense system, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	35.70 Å
Radius of gyration Rg (electron density) rg_electron	35.49 Å
Forward intensity I(0) i0	323507000.00
Molecular weight molecular_weight	141750.0 kDa
Excluded volume excluded_volume	175910 Å³
Envelope volume envelope_volume	235720 Å³
Hydration-shell volume shell_volume	55303 Å³
Envelope diameter envelope_diameter	120.1 Å
Shell Rg shell_rg	42.28 Å
Envelope Rg envelope_rg	35.24 Å
Shape Rg shape_rg	35.49 Å
Total Rg total_rg	35.91 Å
Total atoms total_atoms	9912
Residues n_residues	1256
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	119.6 Å
Rg (real space) rg_real	35.73 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	3.2350e+08
I(0) uncertainty (real space) i0_real_error	5.0640e+06
Rg (reciprocal space) rg_reciprocal	35.72 Å
I(0) (reciprocal space) i0_reciprocal	323500000.0000
Solution quality estimate total_estimate	0.8027
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.185
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	109500000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cysteine desulfurase IscS
Molecular weight formula_weight	45377.6 kDa
EC 编号 ec_number	2.8.1.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9912

MKLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNILNVSFNYVEGESLIMALKDLAVSSGSACTSASLEPSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQGVDLNSIEWAHH

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 polymer

Description description	PptA
Molecular weight formula_weight	30272.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MGSSHHHHHHSSGLVPRGSHMSTNSPRVLCHFSCGAPSAVATKLAIEKYGKDNVTVFNIQITEEHPDNQRFLKECELWFGVPVTTVRNENFKGSIYEVFKQGFIKSPQGAACTTQLKRKVRASFQNPDDIHVFGFTTEEEQRAIDFNERNPSLTTDWVLLDAGFNRNDCLGVLAGVGIGIPQMYKLGYNNNNCVGCVKGGMGYWNKIRKDFPHVFARMAMVEREVGHSLLKDKDGAVWLDELDPDRGRMSKEPDIECSLVCSSTLETLNN

来源 Source

来源生物 organism	Psychrobacter phage vB_PmaS_Y8A
NCBI Class编号 ncbi_taxonomy_id	3017068
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.85 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	363923

fit	/app/data/saxs_computation/1f/21fy/21fy.fit
pddf	/app/data/pr_computation/1f/21fy/21fy.pr.out
profile	/app/data/saxs_computation/1f/21fy/21fy.dat

The cryo-EM structure of IscS-PptA complex

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

Cysteine desulfurase IscS

State in the Current Structure

Other States of the Same Protein in the Database

PptA

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)