SAXSdb — 3gsh

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

Non-specific lipid-transfer protein 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 27–117	Not recorded	ZN ZINC ION × 3 NA SODIUM ION × 2 TFA trifluoroacetic acid × 1 ASY (12E)-10-oxooctadec-12-enoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；0.1M CACODYLATE BUFFER PH6.5, 16% PEG 8000, 0.23M ZINC ACETATE , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.80 Å R-free 0.262
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 27–117	Not recorded	ZN ZINC ION × 1 NA SODIUM ION × 1 TFA trifluoroacetic acid × 1 ASY (12E)-10-oxooctadec-12-enoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；0.1M CACODYLATE BUFFER PH6.5, 16% PEG 8000, 0.23M ZINC ACETATE , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.80 Å R-free 0.262

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 3GSH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BE2 LIPID TRANSFER PROTEIN COMPLEXED WITH PALMITATE, NMR, 10 STRUCTURES Deposited 1998-05-19	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 27–117（91 aa）	Not recorded	PLM PALMITIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 7.2；310 K	Resolution not provided
1JTB LIPID TRANSFER PROTEIN COMPLEXED WITH PALMITOYL COENZYME A, NMR, 16 STRUCTURES Deposited 1996-12-03	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 27–117（91 aa）	Not recorded	COA COENZYME A × 1 PLM PALMITIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 7.2；310 K	Resolution not provided
1LIP BARLEY LIPID TRANSFER PROTEIN (NMR, 4 STRUCTURES) Deposited 1995-09-21	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 27–117（91 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1MID Non-specific lipid transfer protein 1 from barley in complex with L-alfa-lysophosphatidylcholine, Laudoyl Deposited 2002-08-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–117（91 aa）	Not recorded	LAP [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.1M sodium citrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.71 Å R-free 0.212

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLTP1_HORVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 27–117 Author chain B； PDBConstruct 1–91； UniProt 27–117

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	3gsh
Deposition date deposition_date	2009-03-27
Structure title title	Three-dimensional structure of a post translational modified barley LTP1
Keywords keywords	;LTP1, POST-TRANSCRIPTIONAL MODIFICATION, OXYLIPIN, LIPID- BINDING, LIPOPROTEIN, TRANSPORT, LIPID BINDING PROTEIN, Disulfide bond, Lipid-binding ;; 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	17.89 Å
Radius of gyration Rg (electron density) rg_electron	16.94 Å
Forward intensity I(0) i0	9142080.00
Molecular weight molecular_weight	20545.0 kDa
Excluded volume excluded_volume	24928 Å³
Envelope volume envelope_volume	29091 Å³
Hydration-shell volume shell_volume	14885 Å³
Envelope diameter envelope_diameter	59.3 Å
Shell Rg shell_rg	22.33 Å
Envelope Rg envelope_rg	17.07 Å
Shape Rg shape_rg	16.97 Å
Total Rg total_rg	17.70 Å
Total atoms total_atoms	1407
Residues n_residues	182
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	58.0 Å
Rg (real space) rg_real	17.86 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	9.1420e+06
I(0) uncertainty (real space) i0_real_error	1.1710e+05
Rg (reciprocal space) rg_reciprocal	17.86 Å
I(0) (reciprocal space) i0_reciprocal	9142000.0000
Solution quality estimate total_estimate	0.8102
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.337
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1564000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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	Non-specific lipid-transfer protein 1
Molecular weight formula_weight	9705.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1677

LNCGQVDSKMKPCLTYVQGGPGPSGECCNGVRDLHNQAQSSGDRQTVCNCLKGIARGIHNLNLNNAASIPSKCNVNVPYTISPDIDCSRIY

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	trifluoroacetic acid
Molecular weight formula_weight	114.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(12E)-10-oxooctadec-12-enoic acid
Molecular weight formula_weight	296.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	205

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3gsha_
Class class	a — All alpha proteins
Fold Fold fold	a.52 — Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Superfamily Superfamily superfamily	a.52.1 — Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Family Family family	a.52.1.1 — Plant lipid-transfer and hydrophobic proteins

Domain ID domain_id	d3gshb_
Class class	a — All alpha proteins
Fold Fold fold	a.52 — Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Superfamily Superfamily superfamily	a.52.1 — Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Family Family family	a.52.1.1 — Plant lipid-transfer and hydrophobic proteins

CATH v4.4 (2 domains)

Domain ID domain_id	3gshA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	110 — Hydrophobic Seed Protein
Homologous superfamily homologous superfamily	10 — Plant lipid-transfer and hydrophobic proteins

Domain ID domain_id	3gshB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	110 — Hydrophobic Seed Protein
Homologous superfamily homologous superfamily	10 — Plant lipid-transfer and hydrophobic proteins

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8. Citations (1)

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Unit-cell length a length_a	28.740 Å
Unit-cell length b length_b	76.133 Å
Unit-cell length c length_c	39.402 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.560 Å
R factor r_factor	0.1970
R_work r_work	0.1940
R_free r_free	0.2620

fit	/app/data/saxs_computation/gs/3gsh/3gsh.fit
pddf	/app/data/pr_computation/gs/3gsh/3gsh.pr.out
profile	/app/data/saxs_computation/gs/3gsh/3gsh.dat

Three-dimensional structure of a post translational modified barley LTP1

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

Non-specific lipid-transfer 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