SAXSdb — 4txp

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

Vacuolar protein sorting-associated protein VTA1 homolog

Homo sapiens

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 1–162	Fragment：UNP residues 1-162	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate	Resolution 3.01 Å R-free 0.286
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–162	Fragment：UNP residues 1-162	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate	Resolution 3.01 Å R-free 0.286
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–162	Fragment：UNP residues 1-162	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate	Resolution 3.01 Å R-free 0.286

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 4TXP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LXL Lip5(mit)2 Deposited 2012-08-29	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–183（183 aa） Fragment：UNP residues 1-183	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 0.075；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] LIP5(1-183), 25 mM sodium phosphate, 50 mM sodium chloride, 0.5 mM DTT, 0.1 mM EDTA, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
2LXM Lip5-chmp5 Deposited 2012-08-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–168（168 aa） Fragment：UNP residues 1-168	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 75；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] LIP5(1-168), 0.5 mM [U-100% 13C; U-100% 15N] CHMP5(139-195), 25 mM sodium phosphate, 50 mM sodium chloride, 0.5 mM DTT, 0.1 mM EDTA, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
4TXQ Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM Deposited 2014-07-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–162（162 aa） Fragment：UNP residues 1-162	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris	Resolution 2.21 Å R-free 0.227
4TXQ Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM Deposited 2014-07-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–162（162 aa） Fragment：UNP residues 1-162	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris	Resolution 2.21 Å R-free 0.227
4TXR Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM Deposited 2014-07-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–162（162 aa） Fragment：UNP residues 1-162	Not recorded	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；19% PEG 4000, 0.025 M sodium acetate	Resolution 1.00 Å R-free 0.180
4U7E The crystal structure of the complex of LIP5 NTD and IST1 MIM Deposited 2014-07-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–162（162 aa） Fragment：N-terminal domain (UNP residues 1-162)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；30% (w/v) PEG5000MME, 0.1 M ammonium sulfate , 0.1 M MES	Resolution 1.60 Å R-free 0.201

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VTA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–163； UniProt 1–162 Author chain B； PDBConstruct 2–163； UniProt 1–162 Author chain C； PDBConstruct 2–163； UniProt 1–162

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	4txp
Deposition date deposition_date	2014-07-04
Structure title title	Crystal structure of LIP5 N-terminal domain
Keywords keywords	MIT, MIT domain, Protein Transport, ESCRT; PROTEIN TRANSPORT
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	24.78 Å
Radius of gyration Rg (electron density) rg_electron	23.84 Å
Forward intensity I(0) i0	39857100.00
Molecular weight molecular_weight	47281.0 kDa
Excluded volume excluded_volume	58607 Å³
Envelope volume envelope_volume	75962 Å³
Hydration-shell volume shell_volume	26787 Å³
Envelope diameter envelope_diameter	80.7 Å
Shell Rg shell_rg	30.69 Å
Envelope Rg envelope_rg	23.84 Å
Shape Rg shape_rg	23.83 Å
Total Rg total_rg	24.72 Å
Total atoms total_atoms	3334
Residues n_residues	456
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	81.1 Å
Rg (real space) rg_real	24.64 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	3.9860e+07
I(0) uncertainty (real space) i0_real_error	5.4910e+05
Rg (reciprocal space) rg_reciprocal	24.67 Å
I(0) (reciprocal space) i0_reciprocal	39860000.0000
Solution quality estimate total_estimate	0.8157
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.2 Å
Skewness Skewness skewness	0.162
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6862000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4txpA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	270 — Vacuolar protein sorting-associated protein vta1

Domain ID domain_id	4txpB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	270 — Vacuolar protein sorting-associated protein vta1

Domain ID domain_id	4txpC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	270 — Vacuolar protein sorting-associated protein vta1

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8. Citations (1)

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Unit-cell length a length_a	76.381 Å
Unit-cell length b length_b	76.381 Å
Unit-cell length c length_c	355.938 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.010 Å
Low-resolution limit resolution_low	48.460 Å
R factor r_factor	0.2502
R_work r_work	0.2484
R_free r_free	0.2864

Description description	Vacuolar protein sorting-associated protein VTA1 homolog
Molecular weight formula_weight	18792.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3368

Crystal structure of LIP5 N-terminal domain

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

Vacuolar protein sorting-associated protein VTA1 homolog

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

fit	/app/data/saxs_computation/tx/4txp/4txp.fit
pddf	/app/data/pr_computation/tx/4txp/4txp.pr.out
profile	/app/data/saxs_computation/tx/4txp/4txp.dat