SAXSdb — 3btv

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

Galactose/lactose metabolism regulatory protein GAL80

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 1–435 Chain B； UniProt 1–435	Mutation：G301R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；20% PEG 3350, 0.15M Sodium Fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.257

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 3BTV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BTS Crystal structure of a ternary complex of the transcriptional repressor Gal80p (Gal80S0 [G301R]) and the acidic activation domain of Gal4p (aa 854-874) from Saccharomyces cerevisiae with NAD Deposited 2007-12-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–435（435 aa） Chain B 1–435（435 aa）	Mutation：G301R Mutation：G301R	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；20% PEG 3350, 0.15M Sodium fluoride, followed by soaking in NAD to a final concentration of 5mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.70 Å R-free 0.232
3BTU Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K] Deposited 2007-12-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–435（435 aa） Chain B 1–435（435 aa）	Mutation：E351K Mutation：E351K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；290 K；0.1M CAPS, 0.2M NaCl, 20% PEG 8000, 50mM DTT, 4% Gamma-butyrolactone, 0.2M Sodium formate, 9% Sucrose, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.85 Å R-free 0.278
3BTU Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K] Deposited 2007-12-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–435（435 aa） Chain D 1–435（435 aa）	Mutation：E351K Mutation：E351K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；290 K；0.1M CAPS, 0.2M NaCl, 20% PEG 8000, 50mM DTT, 4% Gamma-butyrolactone, 0.2M Sodium formate, 9% Sucrose, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.85 Å R-free 0.278
3BTU Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K] Deposited 2007-12-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–435（435 aa） Chain F 1–435（435 aa）	Mutation：E351K Mutation：E351K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；290 K；0.1M CAPS, 0.2M NaCl, 20% PEG 8000, 50mM DTT, 4% Gamma-butyrolactone, 0.2M Sodium formate, 9% Sucrose, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.85 Å R-free 0.278
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–435（435 aa） Chain B 1–435（435 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

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GAL80_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–438； UniProt 1–435 Author chain B； PDBConstruct 4–438； UniProt 1–435

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	3btv
Deposition date deposition_date	2007-12-31
Structure title title	Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S0)-[G301R]
Keywords keywords	;eukaryotic transcription repressor, Acetylation, Carbohydrate metabolism, DNA-binding, Galactose metabolism, Transcription regulation, transcription ;; TRANSCRIPTION
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	31.72 Å
Radius of gyration Rg (electron density) rg_electron	31.56 Å
Forward intensity I(0) i0	112196000.00
Molecular weight molecular_weight	87483.0 kDa
Excluded volume excluded_volume	110860 Å³
Envelope volume envelope_volume	138490 Å³
Hydration-shell volume shell_volume	38063 Å³
Envelope diameter envelope_diameter	110.2 Å
Shell Rg shell_rg	37.07 Å
Envelope Rg envelope_rg	31.54 Å
Shape Rg shape_rg	31.56 Å
Total Rg total_rg	32.04 Å
Total atoms total_atoms	6174
Residues n_residues	782
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	105.1 Å
Rg (real space) rg_real	31.96 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	1.1220e+08
I(0) uncertainty (real space) i0_real_error	1.8130e+06
Rg (reciprocal space) rg_reciprocal	31.86 Å
I(0) (reciprocal space) i0_reciprocal	112200000.0000
Solution quality estimate total_estimate	0.6353
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.6 Å
Skewness Skewness skewness	0.595
Kurtosis Kurtosis kurtosis	-0.019
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26660000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.977; Smooth: 0.376

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Galactose/lactose metabolism regulatory protein GAL80
Molecular weight formula_weight	48754.4 kDa
Mutation mutation	G301R
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	6380

GSHMDYNKRSSVSTVPNAAPIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGGKPTKKFTKNLVIDIHGTKRDLKLEGDAGFAEISNLVLYYSGTRANDFPLANGQQAPLDPGYDAGKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHYSL

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	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3btvA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3btvA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3btvB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3btvB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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8. Citations (1)

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Unit-cell length a length_a	87.087 Å
Unit-cell length b length_b	103.947 Å
Unit-cell length c length_c	106.179 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	46.610 Å
R factor r_factor	—
R_work r_work	0.2150
R_free r_free	0.2570

fit	/app/data/saxs_computation/bt/3btv/3btv.fit
pddf	/app/data/pr_computation/bt/3btv/3btv.pr.out
profile	/app/data/saxs_computation/bt/3btv/3btv.dat

Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S0)-[G301R]

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

Galactose/lactose metabolism regulatory protein GAL80

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