SAXSdb — 1dc9

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

INTESTINAL FATTY ACID BINDING PROTEIN

Rattus norvegicus

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 1–131	Mutation：V60N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；36-38% PEG 4000, 0.1 M PIPES, 1:1 RATIO WELL AND 4.6 MG/ML PROTEIN IN WATER, pH 7.3, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.228

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 1DC9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A57 THE THREE-DIMENSIONAL STRUCTURE OF A HELIX-LESS VARIANT OF INTESTINAL FATTY ACID BINDING PROTEIN, NMR, 20 STRUCTURES Deposited 1998-02-20	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K	Resolution not provided
1AEL NMR STRUCTURE OF APO INTESTINAL FATTY ACID-BINDING PROTEIN, 20 STRUCTURES Deposited 1996-07-30	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；306 K	Resolution not provided
1ICM ESCHERICHIA COLI-DERIVED RAT INTESTINAL FATTY ACID BINDING PROTEIN WITH BOUND MYRISTATE AT 1.5 A RESOLUTION AND I-FABPARG106-->GLN WITH BOUND OLEATE AT 1.74 A RESOLUTION Deposited 1993-09-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1ICN ESCHERICHIA COLI-DERIVED RAT INTESTINAL FATTY ACID BINDING PROTEIN WITH BOUND MYRISTATE AT 1.5 A RESOLUTION AND I-FABPARG106-->GLN WITH BOUND OLEATE AT 1.74 A RESOLUTION Deposited 1993-09-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	OLA OLEIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å
1IFB REFINED APOPROTEIN STRUCTURE OF RAT INTESTINAL FATTY ACID BINDING PROTEIN PRODUCED IN ESCHERICHIA COLI Deposited 1990-12-05	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.96 Å
1IFC REFINEMENT OF THE STRUCTURE OF RECOMBINANT RAT INTESTINAL FATTY ACID-BINDING APOPROTEIN AT 1.2 ANGSTROMS RESOLUTION Deposited 1991-12-19	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.19 Å
1SA8 THE NMR STRUCTURE OF A STABLE AND COMPACT ALL-beta-SHEET VARIANT OF INTESTINAL FATTY ACID-BINDING PROTEIN Deposited 2004-02-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–8（8 aa） Fragment：D27-GG Chain A 36–131（96 aa） Fragment：D27-GG	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 20 mM potassium phosphate, 135 mM KCl, 10 mM NaCl, 0.5% NaN3；Pressure atmospheric NMR sample composition 1.8 mM protein, 20 mM potassium phosphate, 135 mM KCl, 10 mM NaCl, 0.5% NaN3,95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1T8V The NMR structure of d34a i-fabp: implications for the determinants of ligand binding stoichiometry Deposited 2004-05-13	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Mutation：D34A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM KCl NMR sample composition 20 mM potassium phosphate, 50 mM KCl, 0.5% NaN3, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1URE NMR STRUCTURE OF INTESTINAL FATTY ACID-BINDING PROTEIN COMPLEXED WITH PALMITATE, 20 STRUCTURES Deposited 1996-06-17	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 1–131（131 aa）	Not recorded	PLM PALMITIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 7.2；310 K	Resolution not provided
2IFB CRYSTAL STRUCTURE OF RAT INTESTINAL FATTY-ACID-BINDING PROTEIN. REFINEMENT AND ANALYSIS OF THE ESCHERICHIA COLI-DRIVED PROTEIN WITH BOUND PALMITATE Deposited 1990-12-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	Not recorded	PLM PALMITIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
3AKN X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue Deposited 2010-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–132（131 aa）	Not recorded	11D 11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；30-45% w/v PEG 2000, 0.1M Tris pH 7.0, 0.2M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.257

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FABPI_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 1–131

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	1dc9
Deposition date deposition_date	1999-11-04
Structure title title	PROPERTIES AND CRYSTAL STRUCTURE OF A BETA-BARREL FOLDING MUTANT, V60N INTESTINAL FATTY ACID BINDING PROTEIN (IFABP)
Keywords keywords	FATTY ACID BINDING PROTEIN, INTRACELLULAR LIPID BINDING PROTEIN, MUTANT, BETA- BARREL, LIPID BINDING PROTEIN; 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	15.76 Å
Radius of gyration Rg (electron density) rg_electron	14.35 Å
Forward intensity I(0) i0	4480570.00
Molecular weight molecular_weight	15008.0 kDa
Excluded volume excluded_volume	18815 Å³
Envelope volume envelope_volume	22371 Å³
Hydration-shell volume shell_volume	13279 Å³
Envelope diameter envelope_diameter	46.3 Å
Shell Rg shell_rg	20.15 Å
Envelope Rg envelope_rg	14.33 Å
Shape Rg shape_rg	14.30 Å
Total Rg total_rg	15.68 Å
Total atoms total_atoms	1058
Residues n_residues	131
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	48.1 Å
Rg (real space) rg_real	15.62 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	4.4810e+06
I(0) uncertainty (real space) i0_real_error	4.7580e+04
Rg (reciprocal space) rg_reciprocal	15.63 Å
I(0) (reciprocal space) i0_reciprocal	4481000.0000
Solution quality estimate total_estimate	0.8950
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.014
Kurtosis Kurtosis kurtosis	-0.432
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	903400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dc9a_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.2 — Fatty acid binding protein-like

CATH v4.4 (1 domains)

Domain ID domain_id	1dc9A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (1)

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Unit-cell length a length_a	36.636 Å
Unit-cell length b length_b	52.375 Å
Unit-cell length c length_c	31.594 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2280

Description description	INTESTINAL FATTY ACID BINDING PROTEIN
Molecular weight formula_weight	15030.0 kDa
Mutation mutation	V60N
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1131

PROPERTIES AND CRYSTAL STRUCTURE OF A BETA-BARREL FOLDING MUTANT, V60N INTESTINAL FATTY ACID BINDING PROTEIN (IFABP)

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

INTESTINAL FATTY ACID BINDING 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 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)

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

fit	/app/data/saxs_computation/dc/1dc9/1dc9.fit
pddf	/app/data/pr_computation/dc/1dc9/1dc9.pr.out
profile	/app/data/saxs_computation/dc/1dc9/1dc9.dat