SAXSdb — 1dfw

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

LUNG SURFACTANT PROTEIN B

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 106–130	Fragment：RESIDUES 1-25	No other associated polymer	INFRARED SPECTROSCOPY NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) 10 mM phosphate；Pressure 1 NMR sample composition：This structure was determined using 13-C isotope enhanced FTIR spectroscopy on a family of selectively labeled chemically synthesized peptides. 13-C carbonyl labels included residues 1,3,5,8,10,11,13,14,15,16,18,25. \| Liposomes of 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG)	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 1DFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KMR Solution NMR Structure of Surfactant Protein B (11-25) (SP-B11-25) Deposited 2001-12-17	Different construct Different experimental method Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 211–225（15 aa） Fragment：SEQUENCE DATABASE RESIDUES 211-225, NUMBERED 11-25	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；278 K；Ionic strength (raw mmCIF value) no additional salt or buffer；Pressure ambient NMR sample composition 1.25 mM peptide, 0.1 mM DSS-d6 \| Partially deuterated methanol (CD3OH), 98% D	Resolution not provided
1RG3 SP-B C-terminal peptide in SDS micelles Deposited 2003-11-11	Different construct Different experimental method Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–278（16 aa） Fragment：C-terminal helix	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2 mM SP-B63-78, 200 mM deuterated sodium dodecyl sulfate \| 200 mM deuterated sodium dodecyl sulfate; 90% H2O; 10% D2O; 2 mM DSS	Resolution not provided
1RG4 SP-B C-terminal peptide in organic solvent (HFIP) Deposited 2003-11-11	Different construct Different experimental method Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–278（16 aa） Fragment：C-terminal helix	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；278 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2 mM SP-B63-78 \| 50% H2O; 40% hexafluoroisopropanol; 10% D2O; 2 mM DSS	Resolution not provided
1SSZ Conformational Mapping of Mini-B: An N-terminal/C-terminal Construct of Surfactant Protein B Using 13C-Enhanced Fourier Transform Infrared (FTIR) Spectroscopy Deposited 2004-03-24	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 208–278（71 aa） Fragment：residues 208-218, 263-278	Not recorded	No recorded non-water small molecule	INFRARED SPECTROSCOPY NMR measurement conditions 298 K；Pressure ambient NMR sample composition THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 3,6,7,8,11,13,15,16,18,19,22,25,26,29,30. \| peptide self-film solvated with hexafluoroispropanol:D20, 9:1	Resolution not provided
2DWF NMR structure of Mini-B, an N-terminal- C-terminal construct from human Surfactant Protein B (SP-B), in Sodium dodecyl sulfate (SDS) micelles Deposited 2006-08-11	Different construct Different mutation/modification Different experimental method Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 208–225（18 aa） Fragment：Mini-B Chain A 263–278（16 aa） Fragment：Mini-B	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；318 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition Partially 15N-labelled peptide with 15N labels on Leucine (3, 7, 22, 25, 29, 31), Alanine (6, 13) and Glycine (18); 1.5mM peptide, 150mM SDS, 0.4mM DSS, 90% H2O, 10% D2O \| 150mM SDS, 0.4mM DSS, 90% H2O, 10% D2O	Resolution not provided
2JOU NMR structure of Mini-B, an N-terminal- C-terminal construct from human Surfactant Protein-B (SP-B), in Hexafluoroisopropanol (HFIP) Deposited 2007-03-26	Different construct Different mutation/modification Different experimental method Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 208–225（18 aa） Fragment：Mini-B Chain A 263–278（16 aa） Fragment：Mini-B	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.5 mM Partially 15N-labeled Mini-B, 40 % 98% deuterated HFIP, 50 % H2O, 10 % D2O, 0.4 mM DSS \| 40% HFIP, 50% H2O, 10% D2O	Resolution not provided
2M0H SP-B C-terminal (residues 59-80) peptide in methanol Deposited 2012-10-25	Different construct Different experimental method Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 259–280（22 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 1.2 mM protein, 20 mM TCEP, methanol \| methanol	Resolution not provided
2M1T SP-B C-terminal (residues 59-80) peptide in DPC micelles Deposited 2012-12-06	Different construct Different mutation/modification Different experimental method Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 259–280（22 aa）	Mutation：M65I, M79I	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；315 K；Ionic strength (raw mmCIF value) 130；Pressure ambient NMR sample composition 1.2 mM [U-100% 15N] protein, 80 mM [U-100% 2H] DPC, 1 mM TSP, 50 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PSPB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–25； UniProt 106–130

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	1dfw
Deposition date deposition_date	1999-11-22
Structure title title	CONFORMATIONAL MAPPING OF THE N-TERMINAL SEGMENT OF SURFACTANT PROTEIN B IN LIPID USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR)
Keywords keywords	LUNG SURFACTANT PROTEIN, SAPOSIN, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	INFRARED SPECTROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	10.73 Å
Radius of gyration Rg (electron density) rg_electron	11.18 Å
Forward intensity I(0) i0	9761400.00
Molecular weight molecular_weight	29327.0 kDa
Excluded volume excluded_volume	38568 Å³
Envelope volume envelope_volume	9443 Å³
Hydration-shell volume shell_volume	7173 Å³
Envelope diameter envelope_diameter	46.0 Å
Shell Rg shell_rg	16.80 Å
Envelope Rg envelope_rg	12.96 Å
Shape Rg shape_rg	11.20 Å
Total Rg total_rg	11.59 Å
Total atoms total_atoms	4320
Residues n_residues	250
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	44.0 Å
Rg (real space) rg_real	10.90 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	9.7610e+06
I(0) uncertainty (real space) i0_real_error	1.3170e+05
Rg (reciprocal space) rg_reciprocal	10.90 Å
I(0) (reciprocal space) i0_reciprocal	9761000.0000
Solution quality estimate total_estimate	0.6878
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	7.2 Å
Skewness Skewness skewness	0.425
Kurtosis Kurtosis kurtosis	-0.416
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4118.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.308; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.075; Smooth: 0.939

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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	d1dfwa_
Class class	j — Peptides
Fold Fold fold	j.35 — Transmembrane helical fragments
Superfamily Superfamily superfamily	j.35.1 — Transmembrane helical fragments
Family Family family	j.35.1.1 — Transmembrane helical fragments

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	LUNG SURFACTANT PROTEIN B
Molecular weight formula_weight	2932.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4320

fit	/app/data/saxs_computation/df/1dfw/1dfw.fit
pddf	/app/data/pr_computation/df/1dfw/1dfw.pr.out
profile	/app/data/saxs_computation/df/1dfw/1dfw.dat

CONFORMATIONAL MAPPING OF THE N-TERMINAL SEGMENT OF SURFACTANT PROTEIN B IN LIPID USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR)

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

LUNG SURFACTANT PROTEIN B

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)