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1jbh

Solution structure of cellular retinol binding protein type-I in the ligand-free state

Method: SOLUTION NMR Dmax: 40.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CELLULAR RETINOL-BINDING PROTEIN TYPE I

Rattus norvegicus

UniProt P02696

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 0–134 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 20mM POTASSIUM PHOSPHATE；Pressure AMBIENT NMR sample composition：1.6MM CRBP-I PHOSPHATE BUFFER; 0.05% SODIUM AZIDE 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 1JBH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CRB CRYSTALLOGRAPHIC STUDIES ON A FAMILY OF CELLULAR LIPOPHILIC TRANSPORT PROTEINS. REFINEMENT OF P2 MYELIN PROTEIN AND THE STRUCTURE DETERMINATION AND REFINEMENT OF CELLULAR RETINOL-BINDING PROTEIN IN COMPLEX WITH ALL-TRANS-RETINOL Deposited 1993-02-10 Different construct 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 1–134（134 aa）
Not recorded CD CADMIUM ION × 2 RTL RETINOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.248
1KGL Solution structure of cellular retinol binding protein type-I in complex with all-trans-retinol Deposited 2001-11-27 Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 0–134（135 aa）
Not recorded RTL RETINOL × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM POTASSIUM PHOSPHATE；Pressure AMBIENT
NMR sample composition 1.8MM CRBP-I PHOSPHATE BUFFER; 0.05% SODIUM AZIDE
Resolution not provided
1MX7 Two homologous rat cellular retinol-binding proteins differ in local structure and flexibility Deposited 2002-10-01 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–135（134 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 0.34；Pressure ambient
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.34；Pressure ambient
NMR sample composition 1.0mM ligand free cellular retinol-binding protein I U-[99% 15N, 99% 13C]; 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0mM ligand free cellular retinol-binding protein I U-[99% 15N, 80% 2H]; 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0mM ligand free cellular retinol-binding protein I U-[99% 15N]; 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0mM ligand free cellular retinol-binding protein I U-[99% 15N, 99% 13C]; 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 99.5% D2O | 99.5% D2O
Resolution not provided
1MX8 Two homologous rat cellular retinol-binding proteins differ in local structure and flexibility Deposited 2002-10-01 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–135（134 aa）
Not recorded RTL RETINOL × 1 SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 0.34；Pressure ambient
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.34；Pressure ambient
NMR sample composition 1.0mM cellular retinol-binding protein I U-[99% 15N, 99% 13C] in complex with all-trans retinol (natural isotope abundance); 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0mM cellular retinol-binding protein I U-[99% 15N, 80% 2H] in complex with all-trans retinol (natural isotope abundance); 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name RET1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–135； UniProt 0–134

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1jbh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jbh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1jbh
Deposition date deposition_date2001-06-04
Structure title titleSolution structure of cellular retinol binding protein type-I in the ligand-free state
Keywords keywordsBETA BARREL, RETINOID CARRIER, APO FORM, NMR SPECTROSCOPY, 15N ISOTOPE ENRICHMENT, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.49 Å
Radius of gyration Rg (electron density) rg_electron14.27 Å
Forward intensity I(0) i01428190000.00
Molecular weight molecular_weight316560.0 kDa
Excluded volume excluded_volume393820 ų
Envelope volume envelope_volume30525 ų
Hydration-shell volume shell_volume16132 ų
Envelope diameter envelope_diameter50.8 Å
Shell Rg shell_rg21.99 Å
Envelope Rg envelope_rg15.81 Å
Shape Rg shape_rg14.24 Å
Total Rg total_rg14.47 Å
Total atoms total_atoms44160
Residues n_residues2700
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax40.7 Å
Rg (real space) rg_real14.37 Å
Rg uncertainty (real space) rg_real_error0.14 Å
I(0) (real space) i0_real1.4280e+09
I(0) uncertainty (real space) i0_real_error1.4310e+07
Rg (reciprocal space) rg_reciprocal14.38 Å
I(0) (reciprocal space) i0_reciprocal1428000000.0000
Solution quality estimate total_estimate0.9097
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.1 Å
Skewness Skewness skewness-0.009
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha424300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.916
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1jbha_
Class classb — All beta proteins
Fold Fold foldb.60 — Lipocalins
Superfamily Superfamily superfamilyb.60.1 — Lipocalins
Family Family familyb.60.1.2 — Fatty acid binding protein-like

CATH v4.4 (1 domains)

Domain ID domain_id1jbhA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
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8. Citations (2)

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9. Files and Curves (10)