SAXSdb — 4hp2

▼

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

Thiostrepton

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 56–72 Chain B； UniProt 56–72	Fragment：UNP RESIDUES 56-72 Non-standard monomer：Yes (specific site not provided by mmCIF)	DMF DIMETHYLFORMAMIDE × 8 ETZ diethyl ether × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；DIMETHYLFORMAMID, DIETHYLETHER, pH 7.00, VAPOR DIFFUSION	Resolution 0.64 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 4HP2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E9W Structure of the macrocycle thiostrepton solved using the anomalous dispersive contribution from sulfur Deposited 2000-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；1ML 15.38MG/ML THIOSTREPTON IN CHLOROFORM_ISOAMYL ALCOHOL + 100 MICROL GLYCEROL + 200 MICROL ETHANOL. BATCH METHOD, pH 7.00	Resolution 1.02 Å R-free 0.142
1OLN Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA Deposited 2003-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain B 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 6.2；303 K；Ionic strength (raw mmCIF value) 100 MM NACL, 5 MM MGCL2；Pressure 1	Resolution not provided
2JQ7 Model for thiostrepton binding to the ribosomal L11-RNA Deposited 2007-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain C 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 220；Pressure 1 NMR sample composition 0.3 MM [U-13C, U-15N U-2H] RIBOSOMAL PROTEIN L11, 0.3 MM RIBOSOMAL RNA, 0.3 MM THIOSTREPTON ANTIBIOTIC, 20 MM POTASSIUM PHOSPHATE, 200 MM POTASSIUM CHLORIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2L2W Thiostrepton Deposited 2010-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton, chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
2L2X Thiostrepton, oxidized at CA-CB bond of residue 9 Deposited 2010-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–16（16 aa） Fragment：residues 1-16	Mutation：(DCY)9(BB9) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton (BB9, 9), chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
2L2Y Thiostrepton, epimer form of residue 9 Deposited 2010-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–16（16 aa） Fragment：residues 1-16	Mutation：(DCY)9C Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton (epi,9), chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
2L2Z Thiostrepton, reduced at N-CA bond of residue 14 Deposited 2010-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–17（17 aa）	Mutation：(MH6)14(DSN) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 10 mM thiostrepton (DSN 14), chloroform-d/ethanol-d5 5:1 \| chloroform-d/ethanol-d5 5:1	Resolution not provided
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 5 1–17（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP	Resolution 3.30 Å R-free 0.318
5D8H CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON Deposited 2015-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain D 0–18（19 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 11 NA SODIUM ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 mM Tris-HCl, pH 7.5, 10% PEG 8000, 20% glycerol, 1 mM TCEP (tris(2-carboxyethyl)phosphine), 0.125 mM CTAB	Resolution 2.80 Å R-free 0.245

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

View Construct and Data Evidence

UniProt name	THCL_STRAJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–18； UniProt 56–72 Author chain B； PDBConstruct 2–18； UniProt 56–72

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	4hp2
Deposition date deposition_date	2012-10-23
Structure title title	Invariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution
Keywords keywords	ANTIBIOTIC, THIOPEPTIDE, ANTIBACTERIAL, THIAZOLE, THIAZOLINE, OXAZOLE, RIBOSOME, TRANSLATION INHIBITION; ANTIBIOTIC
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	11.25 Å
Radius of gyration Rg (electron density) rg_electron	11.26 Å
Forward intensity I(0) i0	306849.00
Molecular weight molecular_weight	3558.0 kDa
Excluded volume excluded_volume	4608 Å³
Envelope volume envelope_volume	5794 Å³
Hydration-shell volume shell_volume	5101 Å³
Envelope diameter envelope_diameter	39.1 Å
Shell Rg shell_rg	14.89 Å
Envelope Rg envelope_rg	11.22 Å
Shape Rg shape_rg	11.22 Å
Total Rg total_rg	12.65 Å
Total atoms total_atoms	474
Residues n_residues	10
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	39.1 Å
Rg (real space) rg_real	11.26 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	3.0680e+05
I(0) uncertainty (real space) i0_real_error	3.6470e+03
Rg (reciprocal space) rg_reciprocal	11.26 Å
I(0) (reciprocal space) i0_reciprocal	306800.0000
Solution quality estimate total_estimate	0.7896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	11.9 Å
Skewness Skewness skewness	0.215
Kurtosis Kurtosis kurtosis	-0.449
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22070.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Thiostrepton
Molecular weight formula_weight	1806.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	762

XIASASCTTCICTCSCSSX

Entity 2 Entity 2 non-polymer

Description description	DIMETHYLFORMAMIDE
Molecular weight formula_weight	73.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	diethyl ether
Molecular weight formula_weight	74.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

▶

8. Citations (1)

▶

Unit-cell length a length_a	21.394 Å
Unit-cell length b length_b	22.870 Å
Unit-cell length c length_c	22.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	0.640 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.0678
R_work r_work	0.0678
R_free r_free	—

fit	/app/data/saxs_computation/hp/4hp2/4hp2.fit
pddf	/app/data/pr_computation/hp/4hp2/4hp2.pr.out
profile	/app/data/saxs_computation/hp/4hp2/4hp2.dat

Invariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution

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

Thiostrepton

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