SAXSdb — 1d3u

▼

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

TATA-BINDING PROTEIN

Pyrococcus woesei

UniProt P62001

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–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–181	Fragment：RESIDUES 1-180	DNA 24-MER: BRE+TATA-BOX × 1 DNA 23-MER: BRE+TATA-BOX × 1 TRANSCRIPTION INITIATION FACTOR IIB × 1 （P61999）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；PEG 400, STRONTIUM CHLORIDE, SODIUM CITRATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 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 1D3U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AIS TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI Deposited 1997-04-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–181（181 aa） Fragment：RESIDUES 1 - 181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；HANGING DROP METHOD 8% PEG 8000, 200 MM POTASSIUM PHOSPHATE PH 7.4., vapor diffusion - hanging drop	Resolution 2.10 Å R-free 0.268
1PCZ STRUCTURE OF TATA-BINDING PROTEIN Deposited 1996-10-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa） Chain B 1–191（191 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；50% SATURATED AMMONIUM SULFATE, 0.1 M TRIS PH 7.5, 0.1 M KCL	Resolution 2.20 Å R-free 0.300

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

View Construct and Data Evidence

UniProt name	TBP_PYRWO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–181； UniProt 1–181

TRANSCRIPTION INITIATION FACTOR IIB

Pyrococcus woesei

UniProt P61999

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–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 61–261	Fragment：C-TERMINAL CORE, RESIDUES 62-261	DNA 24-MER: BRE+TATA-BOX × 1 DNA 23-MER: BRE+TATA-BOX × 1 TATA-BINDING PROTEIN × 1 （P62001）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；PEG 400, STRONTIUM CHLORIDE, SODIUM CITRATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 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 1D3U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AIS TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI Deposited 1997-04-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 101–300（200 aa） Fragment：C TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；HANGING DROP METHOD 8% PEG 8000, 200 MM POTASSIUM PHOSPHATE PH 7.4., vapor diffusion - hanging drop	Resolution 2.10 Å R-free 0.268

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

View Construct and Data Evidence

UniProt name	TF2B_PYRWO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–201； UniProt 61–261

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	1d3u
Deposition date deposition_date	1999-10-01
Structure title title	TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI
Keywords keywords	PROTEIN-DNA COMPLEX, TRANSCRIPTION, HYPERTHERMOPHILE, GENE REGULATION-DNA COMPLEX; GENE REGULATION/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	25.46 Å
Radius of gyration Rg (electron density) rg_electron	25.21 Å
Forward intensity I(0) i0	68667200.00
Molecular weight molecular_weight	57261.0 kDa
Excluded volume excluded_volume	68584 Å³
Envelope volume envelope_volume	86344 Å³
Hydration-shell volume shell_volume	28722 Å³
Envelope diameter envelope_diameter	92.4 Å
Shell Rg shell_rg	32.27 Å
Envelope Rg envelope_rg	25.32 Å
Shape Rg shape_rg	25.19 Å
Total Rg total_rg	25.96 Å
Total atoms total_atoms	3967
Residues n_residues	429
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	88.4 Å
Rg (real space) rg_real	25.39 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	6.8670e+07
I(0) uncertainty (real space) i0_real_error	1.0540e+06
Rg (reciprocal space) rg_reciprocal	25.41 Å
I(0) (reciprocal space) i0_reciprocal	68670000.0000
Solution quality estimate total_estimate	0.8741
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13680000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.997

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA 24-MER: BRE+TATA-BOX
Molecular weight formula_weight	7414.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	4147

AGAGTAAAGTTTAAATACTTATAT

Entity 2 Entity 2 polymer

Description description	DNA 23-MER: BRE+TATA-BOX
Molecular weight formula_weight	7003.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TATAAGTATTTAAACTTTACTCT

Entity 3 Entity 3 polymer

Description description	TATA-BINDING PROTEIN
Molecular weight formula_weight	20166.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MVDMSKVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY

来源 Source

来源生物 organism	Pyrococcus woesei
NCBI Class编号 ncbi_taxonomy_id	2262
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	TRANSCRIPTION INITIATION FACTOR IIB
Molecular weight formula_weight	22721.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MVSDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKELVEKLKIKVPIA

来源 Source

来源生物 organism	Pyrococcus woesei
NCBI Class编号 ncbi_taxonomy_id	2262
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d3ua1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1d3ua2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1d3ub1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.2 — Transcription factor IIB (TFIIB), core domain

Domain ID domain_id	d1d3ub2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.2 — Transcription factor IIB (TFIIB), core domain

CATH v4.4 (4 domains)

Domain ID domain_id	1d3uA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1d3uA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1d3uB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	1d3uB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

▶

8. Citations (5)

▶

Unit-cell length a length_a	174.200 Å
Unit-cell length b length_b	174.200 Å
Unit-cell length c length_c	174.200 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	24

Space group space_group	I 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2120
R_work r_work	0.2060
R_free r_free	0.2450

fit	/app/data/saxs_computation/d3/1d3u/1d3u.fit
pddf	/app/data/pr_computation/d3/1d3u/1d3u.pr.out
profile	/app/data/saxs_computation/d3/1d3u/1d3u.dat

TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI

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

TATA-BINDING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

TRANSCRIPTION INITIATION FACTOR IIB

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (5)

9. Files and Curves (10)

Files (7)

Curves (3)