SAXSdb — 1opb

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

CELLULAR RETINOL BINDING PROTEIN II

Rattus rattus

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	RET RETINAL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–133	Not recorded	RET RETINAL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–133	Not recorded	RET RETINAL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–133	Not recorded	RET RETINAL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å

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 1OPB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4M NMR STRUCTURE OF APO CELLULAR RETINOL-BINDING PROTEIN II, 24 STRUCTURES Deposited 1998-12-23	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	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Pressure 1 NMR sample composition 90% WATER/10% D2O	Resolution not provided
1EII NMR STRUCTURE OF HOLO CELLULAR RETINOL-BINDING PROTEIN II Deposited 2000-02-25	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	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 ligand/ion	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

3 other PDB entries and 3 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 Author chain B； PDBConstruct 2–134； UniProt 1–133 Author chain C； PDBConstruct 2–134； UniProt 1–133 Author chain D； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1opb
Deposition date deposition_date	1992-12-09
Structure title title	THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II
Keywords keywords	RETINOL TRANSPORT; RETINOL TRANSPORT
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	29.77 Å
Radius of gyration Rg (electron density) rg_electron	29.03 Å
Forward intensity I(0) i0	64843600.00
Molecular weight molecular_weight	62947.0 kDa
Excluded volume excluded_volume	78709 Å³
Envelope volume envelope_volume	101950 Å³
Hydration-shell volume shell_volume	29305 Å³
Envelope diameter envelope_diameter	95.8 Å
Shell Rg shell_rg	36.35 Å
Envelope Rg envelope_rg	28.39 Å
Shape Rg shape_rg	29.00 Å
Total Rg total_rg	29.87 Å
Total atoms total_atoms	4432
Residues n_residues	532
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	92.3 Å
Rg (real space) rg_real	29.67 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	6.4840e+07
I(0) uncertainty (real space) i0_real_error	9.8600e+05
Rg (reciprocal space) rg_reciprocal	29.72 Å
I(0) (reciprocal space) i0_reciprocal	64850000.0000
Solution quality estimate total_estimate	0.9074
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.109
Kurtosis Kurtosis kurtosis	-0.672
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20820000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CELLULAR RETINOL BINDING PROTEIN II
Molecular weight formula_weight	15606.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4589

MTKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK

来源 Source

来源生物 organism	Rattus rattus
通用名 common_name	black rat
NCBI Class编号 ncbi_taxonomy_id	10117

Entity 2 Entity 2 non-polymer

Description description	RETINAL
Molecular weight formula_weight	284.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1opba_
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

Domain ID domain_id	d1opbb_
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

Domain ID domain_id	d1opbc_
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

Domain ID domain_id	d1opbd_
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 (4 domains)

Domain ID domain_id	1opbA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	1opbB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	1opbC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	1opbD00
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	37.000 Å
Unit-cell length b length_b	64.600 Å
Unit-cell length c length_c	56.000 Å
Unit-cell angle α angle_alpha	92.60 °
Unit-cell angle β angle_beta	102.90 °
Unit-cell angle γ angle_gamma	92.50 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1730
R_work r_work	0.1730
R_free r_free	—

fit	/app/data/saxs_computation/op/1opb/1opb.fit
pddf	/app/data/pr_computation/op/1opb/1opb.pr.out
profile	/app/data/saxs_computation/op/1opb/1opb.dat

THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II

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

CELLULAR RETINOL BINDING PROTEIN II

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