SAXSdb — 5t43

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

Lipocalin-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 19–176	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.4；310 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition：1.0 mM [U-99% 13C; U-99% 15N] Lipocalin, 90 % H2O, 10 % D2O, 50 mM sodium phosphate, 0.04 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 5T43	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XKI Crystal structure of human tear lipocalin/von Ebners gland protein Deposited 2004-09-29	Different construct Different mutation/modification 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 23–176（154 aa）	Mutation：C101S, D158A	ZN ZINC ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；Tris/HCl, Zn-acetate, ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.80 Å R-free 0.254
3EYC New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21 Deposited 2008-10-20	Different construct Different mutation/modification 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 23–176（154 aa） Fragment：residues 5-166	Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274
3EYC New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21 Deposited 2008-10-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–176（154 aa） Fragment：residues 5-166	Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274
3EYC New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21 Deposited 2008-10-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–176（154 aa） Fragment：residues 5-166	Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274
3EYC New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21 Deposited 2008-10-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 23–176（154 aa） Fragment：residues 5-166	Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274
4QAF Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109) Deposited 2014-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–174（152 aa） Fragment：UNP residues 23-174 Chain B 23–174（152 aa） Fragment：UNP residues 23-174	Mutation：;R26V,E27G,F28A,P29L,E30R,M31C,N32L,L33A,E34G,T37I,M39T,L56H,S58K,C61S,E69S,K76I,D80I,K83I,Y87K,I89G,C101S,E104C,H106S,K108V,R111P,K114W,C153S ; Mutation：;R26V,E27G,F28A,P29L,E30R,M31C,N32L,L33A,E34G,T37I,M39T,L56H,S58K,C61S,E69S,K76I,D80I,K83I,Y87K,I89G,C101S,E104C,H106S,K108V,R111P,K114W,C153S ;	OMA 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid × 2 SO4 SULFATE ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；1 M sodium chloride, 0.2 M lithium sulfate, 7.5% w/v dextran sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.242

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

View Construct and Data Evidence

UniProt name	LCN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 19–176

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	5t43
Deposition date deposition_date	2016-08-28
Structure title title	NMR Structure of Apo-form Human Tear Lipocalin
Keywords keywords	TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	15.96 Å
Radius of gyration Rg (electron density) rg_electron	15.30 Å
Forward intensity I(0) i0	1767100000.00
Molecular weight molecular_weight	348430.0 kDa
Excluded volume excluded_volume	432580 Å³
Envelope volume envelope_volume	42330 Å³
Hydration-shell volume shell_volume	19438 Å³
Envelope diameter envelope_diameter	65.1 Å
Shell Rg shell_rg	24.77 Å
Envelope Rg envelope_rg	18.43 Å
Shape Rg shape_rg	15.29 Å
Total Rg total_rg	15.45 Å
Total atoms total_atoms	48540
Residues n_residues	3160
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	55.9 Å
Rg (real space) rg_real	15.85 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.7670e+09
I(0) uncertainty (real space) i0_real_error	2.0930e+07
Rg (reciprocal space) rg_reciprocal	15.86 Å
I(0) (reciprocal space) i0_reciprocal	1767000000.0000
Solution quality estimate total_estimate	0.7577
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.202
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	795800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.618; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5t43a_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.0 — automated matches

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8. Citations (1)

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Description description	Lipocalin-1
Molecular weight formula_weight	17453.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	48540

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 'BL21-Gold(DE3)pLysS AG' ;

fit	/app/data/saxs_computation/t4/5t43/5t43.fit
pddf	/app/data/pr_computation/t4/5t43/5t43.pr.out
profile	/app/data/saxs_computation/t4/5t43/5t43.dat

NMR Structure of Apo-form Human Tear Lipocalin

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

Lipocalin-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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)