SAXSdb — 1rzl

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

NONSPECIFIC LIPID TRANSFER PROTEIN

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 1–91	Fragment：FOUR-HELIX BUNDLE	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

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 1RZL	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 construct 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
1UVA Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza sativa Deposited 2004-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–116（91 aa）	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
1UVB Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza sativa Deposited 2004-01-19	Different construct Different ligand/ion Different experimental conditions 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 experimental conditions 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	NLTP1_ORYSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 1–91

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	1rzl
Deposition date deposition_date	1997-10-09
Structure title title	RICE NONSPECIFIC LIPID TRANSFER PROTEIN
Keywords keywords	LIPID TRANSPORT, ALPHA-HELICAL STRUCTURE; LIPID 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	13.47 Å
Radius of gyration Rg (electron density) rg_electron	12.15 Å
Forward intensity I(0) i0	2288100.00
Molecular weight molecular_weight	9456.0 kDa
Excluded volume excluded_volume	11491 Å³
Envelope volume envelope_volume	12988 Å³
Hydration-shell volume shell_volume	9379 Å³
Envelope diameter envelope_diameter	39.7 Å
Shell Rg shell_rg	17.47 Å
Envelope Rg envelope_rg	12.36 Å
Shape Rg shape_rg	12.11 Å
Total Rg total_rg	13.44 Å
Total atoms total_atoms	649
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

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

Maximum dimension Dmax dmax	40.7 Å
Rg (real space) rg_real	13.38 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	2.2880e+06
I(0) uncertainty (real space) i0_real_error	2.2330e+04
Rg (reciprocal space) rg_reciprocal	13.38 Å
I(0) (reciprocal space) i0_reciprocal	2288000.0000
Solution quality estimate total_estimate	0.8266
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.058
Kurtosis Kurtosis kurtosis	-0.404
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	241700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	717

ITCGQVNSAVGPCLTYARGGAGPSAACCSGVRSLKAAASTTADRRTACNCLKNAARGIKGLNAGNAASIPSKCGVSVPYTISASIDCSRVS

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
Molecular weight formula_weight	221.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	68

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1rzla_
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	1rzlA00
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 (2)

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Unit-cell length a length_a	37.930 Å
Unit-cell length b length_b	37.930 Å
Unit-cell length c length_c	97.870 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2390

fit	/app/data/saxs_computation/rz/1rzl/1rzl.fit
pddf	/app/data/pr_computation/rz/1rzl/1rzl.pr.out
profile	/app/data/saxs_computation/rz/1rzl/1rzl.dat

RICE NONSPECIFIC LIPID TRANSFER PROTEIN

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

NONSPECIFIC LIPID TRANSFER PROTEIN

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