SAXSdb — 3fp4

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

TPR repeat-containing protein YHR117W

Saccharomyces cerevisiae

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 A； UniProt 107–639	Fragment：UNP residues 107-639	Ssa1 × 1 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

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 3FP4	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 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
3FP3 Crystal structure of Tom71 Deposited 2009-01-03	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 107–639（533 aa） Fragment：UNP residues 107-639	Not recorded	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
3LCA Structure of Tom71 complexed with Hsp70 Ssa1 C terminal tail indicating conformational plasticity Deposited 2010-01-10	Different construct 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3fp4
Deposition date deposition_date	2009-01-03
Structure title title	Crystal structure of Tom71 complexed with Ssa1 C-terminal fragment
Keywords keywords	Tom71, Hsp70, Mitochondria, translocation, Chaperone, Phosphoprotein, TPR repeat, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	32.52 Å
Radius of gyration Rg (electron density) rg_electron	32.76 Å
Forward intensity I(0) i0	50160200.00
Molecular weight molecular_weight	56244.0 kDa
Excluded volume excluded_volume	70571 Å³
Envelope volume envelope_volume	90965 Å³
Hydration-shell volume shell_volume	26078 Å³
Envelope diameter envelope_diameter	116.0 Å
Shell Rg shell_rg	35.03 Å
Envelope Rg envelope_rg	32.53 Å
Shape Rg shape_rg	32.81 Å
Total Rg total_rg	32.80 Å
Total atoms total_atoms	3946
Residues n_residues	490
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	114.6 Å
Rg (real space) rg_real	33.06 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	5.0160e+07
I(0) uncertainty (real space) i0_real_error	9.1160e+05
Rg (reciprocal space) rg_reciprocal	32.84 Å
I(0) (reciprocal space) i0_reciprocal	50150000.0000
Solution quality estimate total_estimate	0.7912
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.4 Å
Skewness Skewness skewness	0.578
Kurtosis Kurtosis kurtosis	-0.403
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3350000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.648; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.531; Smooth: 0.807

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	TPR repeat-containing protein YHR117W
Molecular weight formula_weight	60571.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4391

GSHMNGEPDIAQLKGLSPSQRQAYAVQLKNRGNHFFTAKNFNEAIKYYQYAIELDPNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRASANESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILARTMDEKLQATTFAEAAKIQKRLRADPIISAKMELTLARYRAKGML

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ssa1
Molecular weight formula_weight	1202.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

GADNGPTVEEVD

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	264

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8. Citations (1)

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Unit-cell length a length_a	47.820 Å
Unit-cell length b length_b	116.025 Å
Unit-cell length c length_c	150.649 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2104
R_work r_work	0.2077
R_free r_free	0.2613

fit	/app/data/saxs_computation/fp/3fp4/3fp4.fit
pddf	/app/data/pr_computation/fp/3fp4/3fp4.pr.out
profile	/app/data/saxs_computation/fp/3fp4/3fp4.dat

Crystal structure of Tom71 complexed with Ssa1 C-terminal fragment

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

TPR repeat-containing protein YHR117W

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)