SAXSdb — 2nvw

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

Galactose/lactose metabolism regulatory protein GAL80

Kluyveromyces lactis

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 2–457 Chain B； UniProt 2–457	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.25；277 K；20% 2,4-MPD, 0.2M NaCl, 0.1M MES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.245
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–457 Chain B； UniProt 2–457	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.25；277 K；20% 2,4-MPD, 0.2M NaCl, 0.1M MES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.245
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–457 Chain B； UniProt 2–457	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.25；277 K；20% 2,4-MPD, 0.2M NaCl, 0.1M MES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.245

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 2NVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3E1K Crystal structure of Kluyveromyces lactis Gal80p in complex with the acidic activation domain of Gal4p Deposited 2008-08-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–457（457 aa） Chain C 1–457（457 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 20-25% (w/v) pentaerythritol propoxylate 5/4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.289
3E1K Crystal structure of Kluyveromyces lactis Gal80p in complex with the acidic activation domain of Gal4p Deposited 2008-08-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–457（457 aa） Chain G 1–457（457 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 20-25% (w/v) pentaerythritol propoxylate 5/4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.289
3E1K Crystal structure of Kluyveromyces lactis Gal80p in complex with the acidic activation domain of Gal4p Deposited 2008-08-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–457（457 aa） Chain K 1–457（457 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 20-25% (w/v) pentaerythritol propoxylate 5/4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.289
3E1K Crystal structure of Kluyveromyces lactis Gal80p in complex with the acidic activation domain of Gal4p Deposited 2008-08-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 1–457（457 aa） Chain O 1–457（457 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 20-25% (w/v) pentaerythritol propoxylate 5/4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.289

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GAL80_KLULA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–479； UniProt 2–457 Author chain B； PDBConstruct 24–479； UniProt 2–457

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	2nvw
Deposition date deposition_date	2006-11-13
Structure title title	Crystal sctucture of transcriptional regulator Gal80p from kluyveromymes lactis
Keywords keywords	transcription, galactose metabolism, repressor; 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	32.80 Å
Radius of gyration Rg (electron density) rg_electron	32.41 Å
Forward intensity I(0) i0	128270000.00
Molecular weight molecular_weight	92694.0 kDa
Excluded volume excluded_volume	116920 Å³
Envelope volume envelope_volume	147470 Å³
Hydration-shell volume shell_volume	39306 Å³
Envelope diameter envelope_diameter	112.9 Å
Shell Rg shell_rg	37.84 Å
Envelope Rg envelope_rg	32.90 Å
Shape Rg shape_rg	32.42 Å
Total Rg total_rg	32.82 Å
Total atoms total_atoms	6544
Residues n_residues	818
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	114.3 Å
Rg (real space) rg_real	33.10 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	1.2830e+08
I(0) uncertainty (real space) i0_real_error	1.9980e+06
Rg (reciprocal space) rg_reciprocal	32.97 Å
I(0) (reciprocal space) i0_reciprocal	128300000.0000
Solution quality estimate total_estimate	0.8329
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.3 Å
Skewness Skewness skewness	0.595
Kurtosis Kurtosis kurtosis	-0.087
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29350000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.705; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.868; Smooth: 0.840

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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	53643.5 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	6895

MGSSHHHHHHSSENLYFQGHMLANNNKRSKLSTVPSSRPIRVGFVGLTSGKSWVAKTHFLAIQQLSSQFQIVALYNPTLKSSLQTIEQLQLKHATGFDSLESFAQYKDIDMIVVSVKVPEHYEVVKNILEHSSQNLNLRYLYVEWALAASVQQAEELYSISQQRANLQTIICLQGRKSPYIVRAKELISEGCIGDINSIEISGNGGWYGYERPMRSPEYLYDIESGVNLISNSFGHTIDVLQYITGSYFQKINAMISNNIPTQFLLDENGKRTKETISKTCPDHLLFQGILENGKVPVSCSFKGGTPVKKLTKNLVIDIHGTKGDLKIEGDAGFVEISNLVLYFYGIKNGNGSSNGTDNNGAAAIKDKEKVTKSPSPSTGTSEEEQTMEVFHLRNYNSVVGNILRIYESIADYHFLGKPESKSSRGPDDLFASTKFDKQGFRFEGFPTFKDAIILHRLIDAVFRSDKEEKTLDVSKIMI

来源 Source

来源生物 organism	Kluyveromyces lactis
NCBI Class编号 ncbi_taxonomy_id	28985
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	347

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2nvwa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2nvwa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.5 — Glucose 6-phosphate dehydrogenase-like

Domain ID domain_id	d2nvwa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2nvwA01
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	2nvwA02
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	2nvwB01
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	2nvwB02
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	112.200 Å
Unit-cell length b length_b	137.100 Å
Unit-cell length c length_c	72.900 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	30.000 Å
R factor r_factor	0.1970
R_work r_work	0.1950
R_free r_free	0.2450

fit	/app/data/saxs_computation/nv/2nvw/2nvw.fit
pddf	/app/data/pr_computation/nv/2nvw/2nvw.pr.out
profile	/app/data/saxs_computation/nv/2nvw/2nvw.dat

Crystal sctucture of transcriptional regulator Gal80p from kluyveromymes lactis

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