SAXSdb — 1mx7

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

CELLULAR RETINOL-BINDING PROTEIN I, APO

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 2–135	Not recorded	No other associated polymer	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

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 1MX7	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
1JBH Solution structure of cellular retinol binding protein type-I in the ligand-free state Deposited 2001-06-04	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 0–134（135 aa）	Not recorded	No recorded non-water small molecule	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
1KGL Solution structure of cellular retinol binding protein type-I in complex with all-trans-retinol Deposited 2001-11-27	Different construct 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
1MX8 Two homologous rat cellular retinol-binding proteins differ in local structure and flexibility Deposited 2002-10-01	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 1–134； UniProt 2–135

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	1mx7
Deposition date deposition_date	2002-10-01
Structure title title	Two homologous rat cellular retinol-binding proteins differ in local structure and flexibility
Keywords keywords	beta-barrel, helix-turn-helix, Vitamin A, retinol-binding, transport, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.00 Å
Radius of gyration Rg (electron density) rg_electron	14.77 Å
Forward intensity I(0) i0	1695740000.00
Molecular weight molecular_weight	345330.0 kDa
Excluded volume excluded_volume	429680 Å³
Envelope volume envelope_volume	34800 Å³
Hydration-shell volume shell_volume	17532 Å³
Envelope diameter envelope_diameter	52.0 Å
Shell Rg shell_rg	22.87 Å
Envelope Rg envelope_rg	16.39 Å
Shape Rg shape_rg	14.76 Å
Total Rg total_rg	14.89 Å
Total atoms total_atoms	48004
Residues n_residues	2948
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	43.9 Å
Rg (real space) rg_real	14.86 Å
Rg uncertainty (real space) rg_real_error	0.13 Å
I(0) (real space) i0_real	1.6960e+09
I(0) uncertainty (real space) i0_real_error	1.6100e+07
Rg (reciprocal space) rg_reciprocal	14.88 Å
I(0) (reciprocal space) i0_reciprocal	1696000000.0000
Solution quality estimate total_estimate	0.7367
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.0 Å
Skewness Skewness skewness	-0.010
Kurtosis Kurtosis kurtosis	-0.475
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	458100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.975; Smooth: 0.996

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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_id	d1mx7a_
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	1mx7A00
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 (6)

Two Homologous Rat Cellular Retinol-binding Proteins Differ in Local Conformational Flexibility.

J.Mol.Biol. (2003)

PMID: 12850148 · DOI: 10.1016/S0022-2836(03)00629-6 PRIMARY

;Structure and backbone dynamics of apo- and holo-cellular retinal-binding protein in solution ;

J.Biol.Chem. (2002)

DOI: 10.1074/jbc.M201994200

;Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics ;

J.Mol.Biol. (2000)

DOI: 10.1006/jmbi.2000.3883

;The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: comparison with the X-ray structure ;

J.Mol.Biol. (1999)

DOI: 10.1006/jmbi.1999.2544

;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 ;

J.Mol.Biol. (1993)

DOI: 10.1006/jmbi.1993.1238

;Crystal structures of holo and apo-cellular retinol-binding protein II ;

J.Mol.Biol. (1993)

DOI: 10.1006/jmbi.1993.1239

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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	CELLULAR RETINOL-BINDING PROTEIN I, APO
Molecular weight formula_weight	15724.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	48004

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

Two homologous rat cellular retinol-binding proteins differ in local structure and flexibility

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

CELLULAR RETINOL-BINDING PROTEIN I, APO

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

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (6)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/mx/1mx7/1mx7.fit
pddf	/app/data/pr_computation/mx/1mx7/1mx7.pr.out
profile	/app/data/saxs_computation/mx/1mx7/1mx7.dat