SAXSdb — 6d6s

▼

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

Trigger factor

Escherichia coli (strain K12)

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 1–432 Chain B； UniProt 1–432	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；295 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR measurement conditions：pH 7；283 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR measurement conditions：pH 7；295 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：2.2 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] TF, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：0.6 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3] Trigger Factor, 0.6 mM [Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] TF, 100% D2O \| 100% D2O NMR sample composition：0.3 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] RBD, 0.3 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3] PPD-SBD, 100% D2O \| 100% D2O NMR sample composition：0.3 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] RBD, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] PPD, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：0.5 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] SBD, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided

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 6D6S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L1P Solution Structure of the PPIase Domain from E. coli Trigger Factor Deposited 2002-02-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 148–249（102 aa） Fragment：PPIase domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.1M NaCl；Pressure ambient NMR sample composition 2-3mM PPIase domain U-15N; 50mM phosphate buffer; 0.1M NaCl; 0.02% NaN3 \| 90% H2O/10% D2O NMR sample composition 2-3mM PPIase domain; 50mM phosphate buffer; 0.1M NaCl; 0.02% NaN3 \| 90% H2O/10% D2O NMR sample composition 2-3mM PPIase domain; 50mM phosphate buffer; 0.1M NaCl; 0.02% NaN3 \| 100% D2O	Resolution not provided
1OMS Structure determination by MAD: E.coli Trigger Factor binding at the ribosomal exit tunnel. Deposited 2003-02-26	Different construct 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 × 3 PDB declaration: trimeric	Chain A 1–118（118 aa） Fragment：Ribosome binding domain Chain B 1–118（118 aa） Fragment：Ribosome binding domain Chain C 1–118（118 aa） Fragment：Ribosome binding domain	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)	SO4 SULFATE ION × 13 PG4 TETRAETHYLENE GLYCOL × 5 SO2 SULFUR DIOXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；279 K；PEG 2000 MME, PEG 400, ammonium sulfate, sodium acetate, tris, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.30 Å R-free 0.238
1P9Y Ribosome binding of E. coli Trigger Factor mutant F44L. Deposited 2003-05-13	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 1–118（118 aa） Fragment：Ribosome binding domain	Mutation：F44L	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；281 K；PEG 2000 MME, AMMONIUM SULFATE, SODIUM ACETATE, TRIS, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.15 Å R-free 0.247
1P9Y Ribosome binding of E. coli Trigger Factor mutant F44L. Deposited 2003-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–118（118 aa） Fragment：Ribosome binding domain	Mutation：F44L	ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；281 K；PEG 2000 MME, AMMONIUM SULFATE, SODIUM ACETATE, TRIS, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.15 Å R-free 0.247
2VRH Structure of the E. coli trigger factor bound to a translating ribosome Deposited 2008-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–432（432 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 0.5 MG/ML CHLORAMPHENICOL；pH 7.5；50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 0.5 MG/ML CHLORAMPHENICOL cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 19.00 Å
5OWI The dynamic dimer structure of the chaperone Trigger Factor (conformer 1) Deposited 2017-09-01	Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–432（432 aa） Chain B 1–432（432 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 0.3 mM [U-15N; U-2H] Trigger Factor, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1 mM [U-13C; U-15N; U-2H] Trigger Factor, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
5OWJ The dynamic dimer structure of the chaperone Trigger Factor (conformer 2) Deposited 2017-09-01	Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–432（432 aa） Chain B 1–432（432 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 0.3 mM [U-15N; U-2H] Trigger Factor, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1 mM [U-13C; U-15N; U-2H] Trigger Factor, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7D6Z Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor Deposited 2020-10-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric	Chain h 1–117（117 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7D80 Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase, trigger factor, and methionine aminopeptidase Deposited 2020-10-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric	Chain 5 1–432（432 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8ZFI Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factor Deposited 2024-05-07	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 × 50 PDB declaration: 57-meric	Chain V 1–432（432 aa）	Not recorded	ZN ZINC ION × 1 PRO PROLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 140 mM NH4Cl, 25 mM MgCl2, 2 mM DTT cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.90 Å
9WNR Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factor Deposited 2025-09-05	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 × 50 PDB declaration: 57-meric	Chain V 1–432（432 aa）	Not recorded	ZN ZINC ION × 1 PRO PROLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 140 mM NH4Cl, 25 mM MgCl2, 2 mM DTT cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.76 Å

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TIG_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–443； UniProt 1–432 Author chain B； PDBConstruct 12–443； UniProt 1–432

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	6d6s
Deposition date deposition_date	2018-04-22
Structure title title	Solution structure of Trigger Factor dimer
Keywords keywords	protein folding, molecular chaperone, oligomerization, CHAPERONE; CHAPERONE
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.41 Å
Radius of gyration Rg (electron density) rg_electron	34.18 Å
Forward intensity I(0) i0	51442900000.00
Molecular weight molecular_weight	1926800.0 kDa
Excluded volume excluded_volume	2408800 Å³
Envelope volume envelope_volume	273240 Å³
Hydration-shell volume shell_volume	61743 Å³
Envelope diameter envelope_diameter	118.7 Å
Shell Rg shell_rg	43.45 Å
Envelope Rg envelope_rg	35.66 Å
Shape Rg shape_rg	34.17 Å
Total Rg total_rg	34.26 Å
Total atoms total_atoms	271560
Residues n_residues	17280
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	113.7 Å
Rg (real space) rg_real	34.40 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	5.1440e+10
I(0) uncertainty (real space) i0_real_error	9.0350e+08
Rg (reciprocal space) rg_reciprocal	34.41 Å
I(0) (reciprocal space) i0_reciprocal	51440000000.0000
Solution quality estimate total_estimate	0.8151
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.5 Å
Skewness Skewness skewness	0.343
Kurtosis Kurtosis kurtosis	-0.352
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15920000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6d6sa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.241 — Ribosome binding domain-like
Superfamily Superfamily superfamily	d.241.2 — Trigger factor ribosome-binding domain
Family Family family	d.241.2.0 — automated matches

Domain ID domain_id	d6d6sa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.0 — automated matches

Domain ID domain_id	d6d6sa3
Class class	a — All alpha proteins
Fold Fold fold	a.223 — Triger factor/SurA peptide-binding domain-like
Superfamily Superfamily superfamily	a.223.1 — Triger factor/SurA peptide-binding domain-like
Family Family family	a.223.1.0 — automated matches

Domain ID domain_id	d6d6sb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.241 — Ribosome binding domain-like
Superfamily Superfamily superfamily	d.241.2 — Trigger factor ribosome-binding domain
Family Family family	d.241.2.0 — automated matches

Domain ID domain_id	d6d6sb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.0 — automated matches

Domain ID domain_id	d6d6sb3
Class class	a — All alpha proteins
Fold Fold fold	a.223 — Triger factor/SurA peptide-binding domain-like
Superfamily Superfamily superfamily	a.223.1 — Triger factor/SurA peptide-binding domain-like
Family Family family	a.223.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6d6sA01
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

Domain ID domain_id	6d6sB01
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

▶

8. Citations (1)

▶

Description description	Trigger factor
Molecular weight formula_weight	49696.2 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	271560

来源生物 organism	Escherichia coli (strain K12)
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/d6/6d6s/6d6s.fit
pddf	/app/data/pr_computation/d6/6d6s/6d6s.pr.out
profile	/app/data/saxs_computation/d6/6d6s/6d6s.dat

Solution structure of Trigger Factor dimer

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)