SAXSdb — 1ygh

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

PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 99–262	Fragment：HISTONE ACETYLTRANSFERASE DOMAIN	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；400 MM AMMONIUM SULFATE, 20% - 25% PEG 8000, pH 6.0	Resolution 1.90 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 99–262	Fragment：HISTONE ACETYLTRANSFERASE DOMAIN	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；400 MM AMMONIUM SULFATE, 20% - 25% PEG 8000, pH 6.0	Resolution 1.90 Å R-free 0.236

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 1YGH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E6I Bromodomain from GCN5 complexed with acetylated H4 peptide Deposited 2000-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 319–439（121 aa） Fragment：BROMODOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2.2M AMMONIUM SULPHATE, 20% V/V GLYCEROL, 4MM DITHIOTHREITOL, 100 MM HEPES PH 7.5, 125MM NACL 5:1 PEPTIDE:PROTEIN	Resolution 1.87 Å R-free 0.209
6CW2 Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 1 Deposited 2018-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 67–317（251 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.5；294 K；10 mM Tris-Cl pH 8.5, 200 mM Li2SO4, 25% w/v PEG3350	Resolution 2.67 Å R-free 0.284
6CW2 Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 1 Deposited 2018-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 67–317（251 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.5；294 K；10 mM Tris-Cl pH 8.5, 200 mM Li2SO4, 25% w/v PEG3350	Resolution 2.67 Å R-free 0.284
6CW3 Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2 Deposited 2018-03-29	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 H 67–317（251 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7；294 K；100 mM succinic acid pH 7.0, 15% w/v PEG3350	Resolution 1.98 Å R-free 0.227
6CW3 Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2 Deposited 2018-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 67–317（251 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7；294 K；100 mM succinic acid pH 7.0, 15% w/v PEG3350	Resolution 1.98 Å R-free 0.227

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

View Construct and Data Evidence

UniProt name	GCN5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 99–262 Author chain B； PDBConstruct 1–164； UniProt 99–262

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	1ygh
Deposition date deposition_date	1999-05-27
Structure title title	HAT DOMAIN OF GCN5 FROM SACCHAROMYCES CEREVISIAE
Keywords keywords	TRANSCRIPTIONAL REGULATION, HISTONE ACETYLATION, N-ACETYLTRANSFERASE, GCN5 RELATED N-ACETYLTRANSFERASE FAMILY, GENE REGULATION; GENE REGULATION
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	29.84 Å
Radius of gyration Rg (electron density) rg_electron	29.34 Å
Forward intensity I(0) i0	22893200.00
Molecular weight molecular_weight	38643.0 kDa
Excluded volume excluded_volume	48987 Å³
Envelope volume envelope_volume	64928 Å³
Hydration-shell volume shell_volume	18902 Å³
Envelope diameter envelope_diameter	95.5 Å
Shell Rg shell_rg	35.76 Å
Envelope Rg envelope_rg	28.72 Å
Shape Rg shape_rg	29.30 Å
Total Rg total_rg	30.16 Å
Total atoms total_atoms	2714
Residues n_residues	328
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	93.2 Å
Rg (real space) rg_real	30.20 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	2.2630e+07
I(0) uncertainty (real space) i0_real_error	2.9490e+05
Rg (reciprocal space) rg_reciprocal	29.98 Å
I(0) (reciprocal space) i0_reciprocal	22890000.0000
Solution quality estimate total_estimate	0.5582
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.355
Kurtosis Kurtosis kurtosis	-0.921
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	3.5170
Highest regularization parameter α highest_alpha	7882000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.452; Stabil: 0.961; Sysdev: 0.000; Positv: 1.000; Valcen: 0.523; Smooth: 0.500

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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	PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)
Molecular weight formula_weight	19248.5 kDa
EC 编号 ec_number	2.3.1.48
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	2930

KIEFRVVNNDNTKENMMVLTGLKNIFQKQLPKMPKEYIARLVYDRSHLSMAVIRKPLTVVGGITYRPFDKREFAEIVFCAISSTEQVRGYGAHLMNHLKDYVRNTSNIKYFLTYADNYAIGYFKKQGFTKEITLDKSIWMGYIKDYEGGTLMQCSMLPRIRYLD

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	216

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ygha_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yghb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

CATH v4.4 (2 domains)

Domain ID domain_id	1yghA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yghB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

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8. Citations (1)

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Unit-cell length a length_a	40.040 Å
Unit-cell length b length_b	66.510 Å
Unit-cell length c length_c	80.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2360

fit	/app/data/saxs_computation/yg/1ygh/1ygh.fit
pddf	/app/data/pr_computation/yg/1ygh/1ygh.pr.out
profile	/app/data/saxs_computation/yg/1ygh/1ygh.dat

HAT DOMAIN OF GCN5 FROM SACCHAROMYCES CEREVISIAE

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

PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)

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