SAXSdb — 1uva

▼

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

NONSPECIFIC 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–116	Not recorded	MYR MYRISTIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；POLYETHYLENE GLYCOL 600, pH 5.60	Resolution 2.50 Å R-free 0.288

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 1UVA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BV2 LIPID TRANSFER PROTEIN FROM RICE SEEDS, NMR, 14 STRUCTURES Deposited 1998-09-21	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 26–116（91 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；293 K；Pressure 1 NMR sample composition 90% H2O AND 10% D2O	Resolution not provided
1RZL RICE NONSPECIFIC LIPID TRANSFER PROTEIN Deposited 1997-10-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–91（91 aa） Fragment：FOUR-HELIX BUNDLE	Not recorded	SO4 SULFATE ION × 2 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.8	Resolution 1.60 Å R-free 0.239
1UVB Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza sativa Deposited 2004-01-19	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–116（91 aa）	Not recorded	PAM PALMITOLEIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；POLYETHYLENE GLYCOL 600, pH 5.60	Resolution 2.10 Å R-free 0.265
1UVC Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza sativa Deposited 2004-01-19	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–116（91 aa） Chain B 26–116（91 aa）	Not recorded	STE STEARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；POLYETHYLENE GLYCOL 600, pH 5.60	Resolution 2.00 Å R-free 0.258

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

View Construct and Data Evidence

UniProt name	NLT1_ORYSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 26–116

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1uva
Deposition date deposition_date	2004-01-19
Structure title title	Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza sativa
Keywords keywords	LIPID TRANSPORT, LTP 1, PAP 1, RICE, FATTY ACID BINDING; LIPID TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	13.40 Å
Radius of gyration Rg (electron density) rg_electron	11.95 Å
Forward intensity I(0) i0	2038760.00
Molecular weight molecular_weight	9146.0 kDa
Excluded volume excluded_volume	11237 Å³
Envelope volume envelope_volume	12556 Å³
Hydration-shell volume shell_volume	9275 Å³
Envelope diameter envelope_diameter	39.3 Å
Shell Rg shell_rg	17.16 Å
Envelope Rg envelope_rg	12.04 Å
Shape Rg shape_rg	11.96 Å
Total Rg total_rg	13.15 Å
Total atoms total_atoms	632
Residues n_residues	91
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	40.3 Å
Rg (real space) rg_real	13.30 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.0390e+06
I(0) uncertainty (real space) i0_real_error	1.9130e+04
Rg (reciprocal space) rg_reciprocal	13.30 Å
I(0) (reciprocal space) i0_reciprocal	2039000.0000
Solution quality estimate total_estimate	0.8160
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	-0.001
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	179400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1uvaa_
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 (1 domains)

Domain ID domain_id	1uvaA00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	49.650 Å
Unit-cell length b length_b	74.490 Å
Unit-cell length c length_c	49.730 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.080 Å
R factor r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2880

Description description	NONSPECIFIC LIPID TRANSFER PROTEIN 1
Molecular weight formula_weight	8919.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	722

Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza sativa

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

NONSPECIFIC 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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

fit	/app/data/saxs_computation/uv/1uva/1uva.fit
pddf	/app/data/pr_computation/uv/1uva/1uva.pr.out
profile	/app/data/saxs_computation/uv/1uva/1uva.dat