SAXSdb — 3lca

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

Protein TOM71

OrganismNot specified

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：TPR repeats 1-9, UNP residues 107-639	Heat shock protein SSA1 × 1 （P10591） 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

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 3LCA	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 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：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 construct 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
3FP4 Crystal structure of Tom71 complexed with Ssa1 C-terminal fragment Deposited 2009-01-03	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：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

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

View Construct and Data Evidence

UniProt name	TOM71_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–533； UniProt 107–639

Heat shock protein SSA1

OrganismNot specified

UniProt P10591

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 Q； UniProt 631–642	Fragment：UNP residues 631-642	Protein TOM71 × 1 （P38825） 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

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 3LCA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5Z8I Solution structure of the SBDbeta domain of yeast Ssa1 Deposited 2018-01-31	Different construct 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 382–554（173 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 90；Pressure 1 NMR sample composition 1 mM [U-13C; U-15N] Ssa1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5Z8Q Solution structure of the SBDalpha domain of yeast Ssa1 Deposited 2018-02-01	Different construct 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 523–622（100 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 90；Pressure 1 NMR sample composition 1.0 mM [U-13C; U-15N] Ssa1 SBDalpha, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HSP71_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Q； PDBConstruct 1–12； UniProt 631–642

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	3lca
Deposition date deposition_date	2010-01-10
Structure title title	Structure of Tom71 complexed with Hsp70 Ssa1 C terminal tail indicating conformational plasticity
Keywords keywords	;Chaperone, conformational plasticity, Membrane, Mitochondrion, Mitochondrion outer membrane, TPR repeat, Transmembrane, 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	31.17 Å
Radius of gyration Rg (electron density) rg_electron	31.10 Å
Forward intensity I(0) i0	47271700.00
Molecular weight molecular_weight	55346.0 kDa
Excluded volume excluded_volume	69945 Å³
Envelope volume envelope_volume	91830 Å³
Hydration-shell volume shell_volume	27052 Å³
Envelope diameter envelope_diameter	112.8 Å
Shell Rg shell_rg	34.77 Å
Envelope Rg envelope_rg	30.66 Å
Shape Rg shape_rg	31.13 Å
Total Rg total_rg	31.34 Å
Total atoms total_atoms	3905
Residues n_residues	486
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	105.9 Å
Rg (real space) rg_real	31.50 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	4.7270e+07
I(0) uncertainty (real space) i0_real_error	7.6960e+05
Rg (reciprocal space) rg_reciprocal	31.36 Å
I(0) (reciprocal space) i0_reciprocal	47270000.0000
Solution quality estimate total_estimate	0.8371
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.517
Kurtosis Kurtosis kurtosis	-0.422
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3862000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.644; Smooth: 0.872

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein TOM71
Molecular weight formula_weight	60157.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4147

NGEPDIAQLKGLSPSQRQAYAVQLKNRGNHFFTAKNFNEAIKYYQYAIELDPNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRASANESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILARTMDEKLQATTFAEAAKIQKRLRADPIISAKMELTLARYRAKGML

Entity 2 Entity 2 polymer

Description description	Heat shock protein SSA1
Molecular weight formula_weight	1271.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

PEAEGPTVEEVD

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	242

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3lcaA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

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8. Citations (1)

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Unit-cell length a length_a	51.148 Å
Unit-cell length b length_b	97.971 Å
Unit-cell length c length_c	129.102 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	2.190 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2294
R_work r_work	0.2273
R_free r_free	0.2711

fit	/app/data/saxs_computation/lc/3lca/3lca.fit
pddf	/app/data/pr_computation/lc/3lca/3lca.pr.out
profile	/app/data/saxs_computation/lc/3lca/3lca.dat

Structure of Tom71 complexed with Hsp70 Ssa1 C terminal tail indicating conformational plasticity

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

Protein TOM71

State in the Current Structure

Other States of the Same Protein in the Database

Heat shock protein SSA1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 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)