SAXSdb — 2nsc

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

Trigger factor

Thermotoga maritima

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–109	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；293 K；15% PEG 4000, 0.2M potassium chloride, 0.1M MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 2.20 Å R-free 0.260
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–109	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；293 K；15% PEG 4000, 0.2M potassium chloride, 0.1M MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 2.20 Å R-free 0.260

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 2NSC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NSA Structures of and interactions between domains of trigger factor from Themotoga maritim Deposited 2006-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 244–405（162 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；293 K；1.35M ammonium sulfate 0.05M TrisCl, pH 7.4, VAPOR DIFFUSION, temperature 293K	Resolution 1.70 Å R-free 0.252
2NSA Structures of and interactions between domains of trigger factor from Themotoga maritim Deposited 2006-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 244–405（162 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；293 K；1.35M ammonium sulfate 0.05M TrisCl, pH 7.4, VAPOR DIFFUSION, temperature 293K	Resolution 1.70 Å R-free 0.252
2NSB Structures of and interactions between domains of trigger factor from Themotoga maritima Deposited 2006-11-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–109（109 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；14% PEG 4000, 0.2M potassium chloride 0.2M, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.20 Å R-free 0.262
2NSB Structures of and interactions between domains of trigger factor from Themotoga maritima Deposited 2006-11-03	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–109（109 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；14% PEG 4000, 0.2M potassium chloride 0.2M, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.20 Å R-free 0.262
3GTY Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone Deposited 2009-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 1–425（425 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；5-10 % PEG4000, 100 NaOAc, pH 5.5, vapor diffusion, hanging drop, temperature 298K	Resolution 3.40 Å R-free 0.329
3GTY Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone Deposited 2009-03-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–425（425 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；5-10 % PEG4000, 100 NaOAc, pH 5.5, vapor diffusion, hanging drop, temperature 298K	Resolution 3.40 Å R-free 0.329
3GU0 Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone Deposited 2009-03-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–405（405 aa） Fragment：residues 1-405	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；10-15% PEG4000, 200 MgCl2, 100 Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.358
6J0A Crystal structure of E. coli methionine aminopeptidase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex Deposited 2018-12-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 1–405（405 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.20 Å

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TIG_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 1–109

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	2nsc
Deposition date deposition_date	2006-11-03
Structure title title	Structures of and interactions between domains of trigger factor from Themotoga maritima
Keywords keywords	chaperone; CHAPERONE
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	20.54 Å
Radius of gyration Rg (electron density) rg_electron	19.92 Å
Forward intensity I(0) i0	3182040.00
Molecular weight molecular_weight	12767.0 kDa
Excluded volume excluded_volume	16170 Å³
Envelope volume envelope_volume	22791 Å³
Hydration-shell volume shell_volume	11441 Å³
Envelope diameter envelope_diameter	82.3 Å
Shell Rg shell_rg	22.81 Å
Envelope Rg envelope_rg	21.50 Å
Shape Rg shape_rg	19.93 Å
Total Rg total_rg	20.47 Å
Total atoms total_atoms	898
Residues n_residues	109
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	80.6 Å
Rg (real space) rg_real	20.89 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	3.1820e+06
I(0) uncertainty (real space) i0_real_error	4.6280e+04
Rg (reciprocal space) rg_reciprocal	20.83 Å
I(0) (reciprocal space) i0_reciprocal	3182000.0000
Solution quality estimate total_estimate	0.6217
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.5 Å
Skewness Skewness skewness	0.702
Kurtosis Kurtosis kurtosis	0.011
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	961100.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.306; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.160; Smooth: 0.000

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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2nscA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1050 — Trigger factor ribosome-binding domain

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8. Citations (1)

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Unit-cell length a length_a	51.214 Å
Unit-cell length b length_b	75.871 Å
Unit-cell length c length_c	30.514 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	19.620 Å
R factor r_factor	—
R_work r_work	0.1950
R_free r_free	0.2600

Description description	Trigger factor
Molecular weight formula_weight	12818.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1036

Structures of and interactions between domains of trigger factor from Themotoga maritima

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

Trigger factor

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

fit	/app/data/saxs_computation/ns/2nsc/2nsc.fit
pddf	/app/data/pr_computation/ns/2nsc/2nsc.pr.out
profile	/app/data/saxs_computation/ns/2nsc/2nsc.dat