SAXSdb — 1jv4

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

Major urinary protein 2

Mus musculus

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 19–180	Not recorded	CD CADMIUM ION × 7 TZL 2-(SEC-BUTYL)THIAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；60mM CdCl2 and sodium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 1.75 Å R-free 0.265

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 1JV4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DF3 SOLUTION STRUCTURE OF A RECOMBINANT MOUSE MAJOR URINARY PROTEIN Deposited 1999-11-17	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 19–180（162 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；308 K；Ionic strength (raw mmCIF value) 10mM PHOSPHATE；Pressure AMBIENT NMR sample composition UNIFORMLY 15N- AND 13C/15N-LABELLED RECOMBINANT MUP FROM MOUSE; 10MM PHOSPHATE BUFFER	Resolution not provided
1ZND Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex Deposited 2005-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–180（162 aa）	Not recorded	CD CADMIUM ION × 2 PE9 PENTAN-1-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CdCl, malate, HCl, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.204
1ZNE Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex Deposited 2005-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–180（162 aa）	Not recorded	CD CADMIUM ION × 5 HE2 HEXAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CdCl, Malate, HCl, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.224
1ZNG Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex Deposited 2005-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–180（162 aa）	Not recorded	CD CADMIUM ION × 2 HE4 HEPTAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CdCl, malate, HCl, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.216
1ZNH Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex Deposited 2005-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–180（162 aa）	Not recorded	CD CADMIUM ION × 6 OC9 OCTAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CdCl Malate/HCl, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.222
1ZNK Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex Deposited 2005-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–180（162 aa）	Not recorded	CD CADMIUM ION × 2 F09 NONAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CdCl, malate, HCl , pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.255
1ZNL Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex Deposited 2005-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–180（162 aa）	Not recorded	CD CADMIUM ION × 4 DE1 DECAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CADMIUM CHLORIDE, MALATE, HCL, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.226
2DM5 Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor Deposited 2006-04-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–180（162 aa）	Not recorded	CD CADMIUM ION × 4 ODI OCTANE-1,8-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；291 K；CADMIUM CHLORIDE, MALATE, HCL, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.200
2NND The Structural Identification of the Interaction Site and Functional State of RBP for its Membrane Receptor Deposited 2006-10-24	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 19–75（57 aa） Chain A 82–180（99 aa）	Not recorded	CD CADMIUM ION × 4 PRZ 2-ISOBUTYL-3-METHOXYPYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CdCl, malate buffer, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.227
2NNE The Structural Identification of the Interaction Site and Functional State of RBP for its Membrane Receptor Deposited 2006-10-24	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 19–75（57 aa） Chain A 82–180（99 aa）	Not recorded	CD CADMIUM ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；CdCl, malate buffer, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.240

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MUP2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 19–180

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	1jv4
Deposition date deposition_date	2001-08-28
Structure title title	Crystal structure of recombinant major mouse urinary protein (rmup) at 1.75 A resolution
Keywords keywords	lipocalin recombinant beta barrel, TRANSPORT PROTEIN; TRANSPORT 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	16.73 Å
Radius of gyration Rg (electron density) rg_electron	14.95 Å
Forward intensity I(0) i0	7877980.00
Molecular weight molecular_weight	18864.0 kDa
Excluded volume excluded_volume	22720 Å³
Envelope volume envelope_volume	26012 Å³
Hydration-shell volume shell_volume	14539 Å³
Envelope diameter envelope_diameter	53.5 Å
Shell Rg shell_rg	21.05 Å
Envelope Rg envelope_rg	15.19 Å
Shape Rg shape_rg	14.76 Å
Total Rg total_rg	16.47 Å
Total atoms total_atoms	1278
Residues n_residues	157
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	61.5 Å
Rg (real space) rg_real	16.60 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	7.8780e+06
I(0) uncertainty (real space) i0_real_error	1.0170e+05
Rg (reciprocal space) rg_reciprocal	16.61 Å
I(0) (reciprocal space) i0_reciprocal	7878000.0000
Solution quality estimate total_estimate	0.7311
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.041
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1819000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.509; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Major urinary protein 2
Molecular weight formula_weight	18733.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1449

EEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGNFRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADKTEKAGEYSVTYDGFNTFTIPKTDYDNFLMAHLINEKDGETFQLMGLYGREPDLSSDIKERFAQLCEEHGILRENIIDLSNANRCLQARE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	2-(SEC-BUTYL)THIAZOLE
Molecular weight formula_weight	141.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1jv4a_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

CATH v4.4 (1 domains)

Domain ID domain_id	1jv4A00
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 (3)

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Unit-cell length a length_a	37.140 Å
Unit-cell length b length_b	55.790 Å
Unit-cell length c length_c	37.670 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.24 °
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	1.750 Å
Low-resolution limit resolution_low	14.000 Å
R factor r_factor	—
R_work r_work	0.2060
R_free r_free	0.2650

fit	/app/data/saxs_computation/jv/1jv4/1jv4.fit
pddf	/app/data/pr_computation/jv/1jv4/1jv4.pr.out
profile	/app/data/saxs_computation/jv/1jv4/1jv4.dat

Crystal structure of recombinant major mouse urinary protein (rmup) at 1.75 A resolution

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

Major urinary protein 2

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