SAXSdb — 8p5p

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

Tectonin beta-propeller repeat-containing protein 1

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 60–173	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；25% (w/v) PEG 6,000 100 mM LiCl 100 mM HEPES pH 75.	Resolution 1.90 Å R-free 0.208
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 60–173	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；25% (w/v) PEG 6,000 100 mM LiCl 100 mM HEPES pH 75.	Resolution 1.90 Å R-free 0.208
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 60–173	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；25% (w/v) PEG 6,000 100 mM LiCl 100 mM HEPES pH 75.	Resolution 1.90 Å R-free 0.208

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 8P5P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4TQ1 Crystal structure of human ATG5-TECAIR Deposited 2014-06-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 503–540（38 aa） Fragment：UNP residues 503-540	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；MPD, PEG 1000, PEG 3350, alcohols, MES-imdazole	Resolution 1.80 Å R-free 0.222

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TCPR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–116； UniProt 60–173 Author chain B； PDBConstruct 3–116； UniProt 60–173 Author chain C； PDBConstruct 3–116； UniProt 60–173

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	8p5p
Deposition date deposition_date	2023-05-24
Structure title title	Structure of TECPR1 N-terminal DysF domain
Keywords keywords	Sphingomyelin binding, LIPID BINDING PROTEIN; LIPID BINDING 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	24.75 Å
Radius of gyration Rg (electron density) rg_electron	24.40 Å
Forward intensity I(0) i0	27189100.00
Molecular weight molecular_weight	39433.0 kDa
Excluded volume excluded_volume	49030 Å³
Envelope volume envelope_volume	61838 Å³
Hydration-shell volume shell_volume	22509 Å³
Envelope diameter envelope_diameter	95.7 Å
Shell Rg shell_rg	29.74 Å
Envelope Rg envelope_rg	24.66 Å
Shape Rg shape_rg	24.41 Å
Total Rg total_rg	25.02 Å
Total atoms total_atoms	5432
Residues n_residues	306
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	93.7 Å
Rg (real space) rg_real	24.90 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	2.7190e+07
I(0) uncertainty (real space) i0_real_error	4.4650e+05
Rg (reciprocal space) rg_reciprocal	24.86 Å
I(0) (reciprocal space) i0_reciprocal	27190000.0000
Solution quality estimate total_estimate	0.8104
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.8 Å
Skewness Skewness skewness	0.520
Kurtosis Kurtosis kurtosis	0.039
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3516000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.622; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.683; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tectonin beta-propeller repeat-containing protein 1
Molecular weight formula_weight	14086.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5736

GAASDVPIRRREEAYENQRWNPMGGFCEKLLLSDRWGWSDVSGLQHRPLDRVALPSPHWEWESDWYVDENFGGEPTEKGGWTYAIDFPATYTKDKKWNSCVRRRKWIRYRRYKSRD

来源 Source

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

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	304

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8. Citations (1)

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Unit-cell length a length_a	75.715 Å
Unit-cell length b length_b	75.715 Å
Unit-cell length c length_c	122.855 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	18

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	44.830 Å
R factor r_factor	0.1681
R_work r_work	0.1661
R_free r_free	0.2084

fit	/app/data/saxs_computation/p5/8p5p/8p5p.fit
pddf	/app/data/pr_computation/p5/8p5p/8p5p.pr.out
profile	/app/data/saxs_computation/p5/8p5p/8p5p.dat

Structure of TECPR1 N-terminal DysF domain

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

Tectonin beta-propeller repeat-containing protein 1

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