SAXSdb — 2j49

▼

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

TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 5

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 147–290	Fragment：N-TERMINAL DOMAIN, RESIDUES 147-290	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；0.05 M CACODYLATE PH 6.5,2.4 M NA FORMATE	Resolution 2.30 Å R-free 0.270

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 2J49	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 1–798（798 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.90 Å
6T9K SAGA Core module Deposited 2019-10-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–798（798 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.30 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TAF5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–148； UniProt 147–290

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	2j49
Deposition date deposition_date	2006-08-28
Structure title title	Crystal structure of yeast TAF5 N-terminal domain
Keywords keywords	TRANSCRIPTION, NUCLEAR PROTEIN, TRANSCRIPTION REGULATION, TAF5, TFIID, WD REPEAT, INITIATION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.04 Å
Radius of gyration Rg (electron density) rg_electron	14.54 Å
Forward intensity I(0) i0	4408340.00
Molecular weight molecular_weight	15746.0 kDa
Excluded volume excluded_volume	20046 Å³
Envelope volume envelope_volume	22534 Å³
Hydration-shell volume shell_volume	13103 Å³
Envelope diameter envelope_diameter	50.1 Å
Shell Rg shell_rg	20.36 Å
Envelope Rg envelope_rg	14.88 Å
Shape Rg shape_rg	14.51 Å
Total Rg total_rg	15.85 Å
Total atoms total_atoms	1116
Residues n_residues	134
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	50.5 Å
Rg (real space) rg_real	15.93 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	4.4080e+06
I(0) uncertainty (real space) i0_real_error	4.6190e+04
Rg (reciprocal space) rg_reciprocal	15.94 Å
I(0) (reciprocal space) i0_reciprocal	4408000.0000
Solution quality estimate total_estimate	0.8876
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.108
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	715100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.976

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2j49a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

CATH v4.4 (1 domains)

Domain ID domain_id	2j49A00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	91.340 Å
Unit-cell length b length_b	91.340 Å
Unit-cell length c length_c	55.240 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.640 Å
R factor r_factor	0.2210
R_work r_work	0.2150
R_free r_free	0.2700

Description description	TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 5
Molecular weight formula_weight	17282.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1153

Crystal structure of yeast TAF5 N-terminal domain

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

TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 5

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

fit	/app/data/saxs_computation/j4/2j49/2j49.fit
pddf	/app/data/pr_computation/j4/2j49/2j49.pr.out
profile	/app/data/saxs_computation/j4/2j49/2j49.dat