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1b4m

NMR STRUCTURE OF APO CELLULAR RETINOL-BINDING PROTEIN II, 24 STRUCTURES

Method: SOLUTION NMR Dmax: 46.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CELLULAR RETINOL-BINDING PROTEIN II

Rattus norvegicus

UniProt P06768

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 1–133 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.4；298 K；Pressure 1 NMR sample composition：90% WATER/10% D2O 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 1B4M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EII NMR STRUCTURE OF HOLO CELLULAR RETINOL-BINDING PROTEIN II Deposited 2000-02-25 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–134（134 aa）
Not recorded RTL RETINOL × 1 SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 0.081；Pressure ambient
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.079；Pressure ambient
NMR sample composition 1.5 mM CELLULAR RETINOL-BINDING PROTEIN II U-15N,13C, complexed with all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer | 95% H2O/5% D2O
NMR sample composition 1.5 mM CELLULAR RETINOL-BINDING PROTEIN II U-15N,13C, complexed with all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer | 99% D2O
NMR sample composition 1.5 mM CELLULAR RETINOL-BINDING PROTEIN II U-15N, complexed with all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer | 95% H2O/5% D2O
NMR sample composition 0.2 mM CELLULAR RETINOL-BINDING PROTEIN II natural abundance, complexed with (2,3,6,7,8,9,10,11,19-13C)-all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer | 99% D2O
Resolution not provided
1OPA THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II Deposited 1992-12-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–133（133 aa）
Chain B 1–133（133 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1OPB THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II Deposited 1992-12-09 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 1–133（133 aa）
Not recorded RET RETINAL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1OPB THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II Deposited 1992-12-09 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–133（133 aa）
Not recorded RET RETINAL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1OPB THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II Deposited 1992-12-09 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–133（133 aa）
Not recorded RET RETINAL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1OPB THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II Deposited 1992-12-09 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–133（133 aa）
Not recorded RET RETINAL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RET2_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–134； UniProt 1–133

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 1b4m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b4m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b4m
Deposition date deposition_date1998-12-23
Structure title titleNMR STRUCTURE OF APO CELLULAR RETINOL-BINDING PROTEIN II, 24 STRUCTURES
Keywords keywordsCELLULAR RETINOL-BINDING PROTEIN, LIPID TRANSPORT, CRBP II, LIPID-BINDING PROTEIN, RETINOL TRANSPORT; RETINOL TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.72 Å
Radius of gyration Rg (electron density) rg_electron14.49 Å
Forward intensity I(0) i02014260000.00
Molecular weight molecular_weight374010.0 kDa
Excluded volume excluded_volume464490 ų
Envelope volume envelope_volume32370 ų
Hydration-shell volume shell_volume16641 ų
Envelope diameter envelope_diameter55.5 Å
Shell Rg shell_rg22.57 Å
Envelope Rg envelope_rg16.30 Å
Shape Rg shape_rg14.45 Å
Total Rg total_rg14.70 Å
Total atoms total_atoms52032
Residues n_residues3216
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 dmax46.4 Å
Rg (real space) rg_real14.60 Å
Rg uncertainty (real space) rg_real_error0.20 Å
I(0) (real space) i0_real2.0140e+09
I(0) uncertainty (real space) i0_real_error2.0250e+07
Rg (reciprocal space) rg_reciprocal14.61 Å
I(0) (reciprocal space) i0_reciprocal2014000000.0000
Solution quality estimate total_estimate0.8946
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.4 Å
Skewness Skewness skewness0.036
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha393000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.995
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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_idd1b4ma_
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_id1b4mA00
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 (5)

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9. Files and Curves (10)