SAXSdb — 3v5r

▼

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

Protein GAL3

Saccharomyces cerevisiae

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 17–520 Chain B； UniProt 17–520	Not recorded	SO4 SULFATE ION × 27	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.202
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 17–520 Chain B； UniProt 17–520	Not recorded	SO4 SULFATE ION × 54	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.202
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 17–520 Chain B； UniProt 17–520	Not recorded	SO4 SULFATE ION × 54	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.202
4	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 17–520 Chain B； UniProt 17–520	Not recorded	SO4 SULFATE ION × 54	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；290 K；10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.202

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 3V5R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3V2U Crystal structure of the yeast GAL regulon complex of the repressor, Gal80p, and the transducer, Gal3p, with galactose and ATP Deposited 2011-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–520（519 aa） Chain D 2–520（519 aa）	Not recorded	GOL GLYCEROL × 2 MG MAGNESIUM ION × 2 GLA alpha-D-galactopyranose × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；290 K；10% PEG 3350, 0.1M di-sodium succinate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.197

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GAL3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–505； UniProt 17–520 Author chain B； PDBConstruct 2–505； UniProt 17–520

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3v5r
Deposition date deposition_date	2011-12-16
Structure title title	Crystal structure of the unliganded form of Gal3p
Keywords keywords	GHMP superfamily, Transcription transducer, Gal80p, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	31.71 Å
Radius of gyration Rg (electron density) rg_electron	30.93 Å
Forward intensity I(0) i0	217529000.00
Molecular weight molecular_weight	113790.0 kDa
Excluded volume excluded_volume	140580 Å³
Envelope volume envelope_volume	174660 Å³
Hydration-shell volume shell_volume	45514 Å³
Envelope diameter envelope_diameter	104.6 Å
Shell Rg shell_rg	39.29 Å
Envelope Rg envelope_rg	30.88 Å
Shape Rg shape_rg	30.93 Å
Total Rg total_rg	31.59 Å
Total atoms total_atoms	7962
Residues n_residues	996
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.9 Å
Rg (real space) rg_real	31.56 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	2.1750e+08
I(0) uncertainty (real space) i0_real_error	3.1180e+06
Rg (reciprocal space) rg_reciprocal	31.63 Å
I(0) (reciprocal space) i0_reciprocal	217500000.0000
Solution quality estimate total_estimate	0.9008
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.1 Å
Skewness Skewness skewness	0.189
Kurtosis Kurtosis kurtosis	-0.485
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	93730000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.878

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein GAL3
Molecular weight formula_weight	56514.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8865

SRSFEQKHLAVVDAFFQTYHVKPDFIARSPGRVNLIGEHIDYCDFSVLPLAIDVDMLCAVKILDEKNPSITLTNADPKFAQRKFDLPLDGSYMAIDPSVSEWSNYFKCGLHVAHSYLKKIAPERFNNTPLVGAQIFCQSDIPTGGGLSSAFTCAAALATIRANMGKNFDISKKDLTRITAVAEHYVGVNNGGMDQATSVYGEEDHALYVEFRPKLKATPFKFPQLKNHEISFVIANTLVKSNKFETAPTNYNLRVIEVTVAANALATRYSVALPSHKDNSNSERGNLRDFMDAYYARYENQAQPWNGDIGTGIERLLKMLQLVEESFSRKKSGFTVHEASTALNCSREEFTRDYLTTFPVRFQVLKLYQRAKHVYSESLRVLKALKMMTSATFHTDEDFFTDFGRLMNESQASCDKLYECSCIETNQICSIALANGSFGSRLTGAGWGGCTIHLVPSGANGNVEQVRKALIEKFYNVRYPDLTDEELKDAIIVSKPALGTCLYEQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	27

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	778

▼

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3v5rA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3v5rA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3170 —

Domain ID domain_id	3v5rA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	3v5rB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3v5rB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3170 —

Domain ID domain_id	3v5rB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	340 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	153.359 Å
Unit-cell length b length_b	153.359 Å
Unit-cell length c length_c	118.591 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.099 Å
Low-resolution limit resolution_low	46.907 Å
R factor r_factor	0.1713
R_work r_work	0.1697
R_free r_free	0.2016

fit	/app/data/saxs_computation/v5/3v5r/3v5r.fit
pddf	/app/data/pr_computation/v5/3v5r/3v5r.pr.out
profile	/app/data/saxs_computation/v5/3v5r/3v5r.dat

Crystal structure of the unliganded form of Gal3p

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

Protein GAL3

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