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3gty

Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

Method: X-RAY DIFFRACTION Dmax: 112.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Trigger factor

Thermotoga maritima

UniProt Q9WZF8

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain X； UniProt 1–425 Not recorded 30S ribosomal protein S7 × 1 （P38526） 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain X； UniProt 1–425 Not recorded No other associated polymer 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

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 3GTY 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 oligomeric state 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 construct 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 construct Different oligomeric state 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
2NSC Structures of and interactions between domains of trigger factor from Themotoga maritima Deposited 2006-11-03 Different construct 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 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
2NSC Structures of and interactions between domains of trigger factor from Themotoga maritima Deposited 2006-11-03 Different construct Different oligomeric state 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 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
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 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 X； PDBConstruct 1–425； UniProt 1–425

30S ribosomal protein S7

Thermotoga maritima

UniProt P38526

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain S； UniProt 9–155 Fragment：sequence database residues 9-155 Trigger factor × 1 （Q9WZF8） 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain S； UniProt 9–155 Fragment：sequence database residues 9-155 No other associated polymer 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

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 RS7_THEMA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain S； PDBConstruct 3–149； UniProt 9–155

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3gty

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3gty
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3gty
Deposition date deposition_date2009-03-28
Structure title titlePromiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone
Keywords keywords;Chaperone-Client Complex, Cell cycle, Cell division, Chaperone, Isomerase, Rotamase, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Chaperone-Ribosomal protein COMPLEX ;; Chaperone/Ribosomal protein
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.61 Å
Radius of gyration Rg (electron density) rg_electron32.55 Å
Forward intensity I(0) i067774400.00
Molecular weight molecular_weight65477.0 kDa
Excluded volume excluded_volume82618 ų
Envelope volume envelope_volume125280 ų
Hydration-shell volume shell_volume35033 ų
Envelope diameter envelope_diameter120.0 Å
Shell Rg shell_rg35.92 Å
Envelope Rg envelope_rg32.40 Å
Shape Rg shape_rg32.54 Å
Total Rg total_rg32.91 Å
Total atoms total_atoms4610
Residues n_residues561
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.7 Å
Rg (real space) rg_real34.21 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real6.8040e+07
I(0) uncertainty (real space) i0_real_error8.3530e+05
Rg (reciprocal space) rg_reciprocal32.78 Å
I(0) (reciprocal space) i0_reciprocal67770000.0000
Solution quality estimate total_estimate0.6310
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.1 Å
Skewness Skewness skewness0.613
Kurtosis Kurtosis kurtosis-0.018
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha2.6780
Highest regularization parameter α highest_alpha5918000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.778; Stabil: 0.878; Sysdev: 0.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.338
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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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3gtyS00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology455 — Ribosomal Protein S7
Homologous superfamily homologous superfamily10 — Ribosomal protein S7/S5
Domain ID domain_id3gtyX01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1050 — Trigger factor ribosome-binding domain
Domain ID domain_id3gtyX02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily30 — Transcription elongation factor, GreA/GreB, C-terminal domain
Domain ID domain_id3gtyX03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3120 — Trigger factor, domain 2
Homologous superfamily homologous superfamily10 — Trigger factor, C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)