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3fp3

Crystal structure of Tom71

Method: X-RAY DIFFRACTION Dmax: 112.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TPR repeat-containing protein YHR117W

Saccharomyces cerevisiae

UniProt P38825

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 107–639 Fragment：UNP residues 107-639 SO4 SULFATE ION × 3 CL CHLORIDE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG4K, NaCl 0.15M, Tris 10mM, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.98 Å R-free 0.227

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 3FP3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FP2 Crystal structure of Tom71 complexed with Hsp82 C-terminal fragment Deposited 2009-01-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 107–639（533 aa） Fragment：UNP residues 107-639
Not recorded CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG6K, Ethylene Glyco 5%, NaCl 0.15M, Tris 10mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.98 Å R-free 0.236
3FP4 Crystal structure of Tom71 complexed with Ssa1 C-terminal fragment Deposited 2009-01-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 107–639（533 aa） Fragment：UNP residues 107-639
Not recorded CL CHLORIDE ION × 11 NA SODIUM ION × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG6K, 5% Ethylene Glyco, 0.15M NaCl, Tris 10mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.14 Å R-free 0.261
3LCA Structure of Tom71 complexed with Hsp70 Ssa1 C terminal tail indicating conformational plasticity Deposited 2010-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 107–639（533 aa） Fragment：TPR repeats 1-9, UNP residues 107-639
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% Ethylene Glycol, 20% PEG 6000, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.19 Å R-free 0.271

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name YHR7_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–537； UniProt 107–639

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 3fp3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fp3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fp3
Deposition date deposition_date2009-01-03
Structure title titleCrystal structure of Tom71
Keywords keywordsTom71, Chaperone, Mitochondria, translocation, Phosphoprotein, TPR repeat, TRANSPORT PROTEIN; TRANSPORT 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_guinier31.79 Å
Radius of gyration Rg (electron density) rg_electron31.90 Å
Forward intensity I(0) i050840800.00
Molecular weight molecular_weight56626.0 kDa
Excluded volume excluded_volume71146 ų
Envelope volume envelope_volume92210 ų
Hydration-shell volume shell_volume26863 ų
Envelope diameter envelope_diameter113.4 Å
Shell Rg shell_rg34.68 Å
Envelope Rg envelope_rg32.07 Å
Shape Rg shape_rg31.92 Å
Total Rg total_rg32.11 Å
Total atoms total_atoms3984
Residues n_residues498
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 dmax112.0 Å
Rg (real space) rg_real32.27 Å
Rg uncertainty (real space) rg_real_error1.26 Å
I(0) (real space) i0_real5.0840e+07
I(0) uncertainty (real space) i0_real_error8.8370e+05
Rg (reciprocal space) rg_reciprocal32.07 Å
I(0) (reciprocal space) i0_reciprocal50830000.0000
Solution quality estimate total_estimate0.8083
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.4 Å
Skewness Skewness skewness0.610
Kurtosis Kurtosis kurtosis-0.280
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4042000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.669; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.673; Smooth: 0.823
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3fp3A01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
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8. Citations (1)

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9. Files and Curves (10)