SAXSdb — 1pcz

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–191 Chain B； UniProt 1–191	Not recorded	No other associated polymer	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

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 1PCZ	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 mutation/modification Different oligomeric state 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
1D3U TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI Deposited 1999-10-01	Different construct Different mutation/modification Different oligomeric state 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 1-180	Not recorded	No recorded non-water small molecule	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

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–191； UniProt 1–191 Author chain B； PDBConstruct 1–191； UniProt 1–191

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	1pcz
Deposition date deposition_date	1996-10-04
Structure title title	STRUCTURE OF TATA-BINDING PROTEIN
Keywords keywords	TRANSCRIPTION REGULATION, DNA-BINDING PROTEIN, NUCLEAR PROTEIN, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	24.43 Å
Radius of gyration Rg (electron density) rg_electron	24.03 Å
Forward intensity I(0) i0	24843800.00
Molecular weight molecular_weight	40552.0 kDa
Excluded volume excluded_volume	51834 Å³
Envelope volume envelope_volume	59317 Å³
Hydration-shell volume shell_volume	22111 Å³
Envelope diameter envelope_diameter	92.4 Å
Shell Rg shell_rg	29.54 Å
Envelope Rg envelope_rg	24.34 Å
Shape Rg shape_rg	24.02 Å
Total Rg total_rg	24.77 Å
Total atoms total_atoms	2852
Residues n_residues	366
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	88.3 Å
Rg (real space) rg_real	24.65 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	2.4840e+07
I(0) uncertainty (real space) i0_real_error	3.6940e+05
Rg (reciprocal space) rg_reciprocal	24.60 Å
I(0) (reciprocal space) i0_reciprocal	24840000.0000
Solution quality estimate total_estimate	0.8148
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.610
Kurtosis Kurtosis kurtosis	0.049
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9552000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.649; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.672; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pcza1
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	d1pcza2
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	d1pczb1
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	d1pczb2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1pczA01
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	1pczA02
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	1pczB01
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	1pczB02
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

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8. Citations (1)

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Unit-cell length a length_a	89.620 Å
Unit-cell length b length_b	89.620 Å
Unit-cell length c length_c	141.280 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.3000

Description description	TATA-BINDING PROTEIN
Molecular weight formula_weight	21337.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3120

STRUCTURE OF TATA-BINDING PROTEIN

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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pyrococcus woesei
NCBI Class编号 ncbi_taxonomy_id	2262
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	268

fit	/app/data/saxs_computation/pc/1pcz/1pcz.fit
pddf	/app/data/pr_computation/pc/1pcz/1pcz.pr.out
profile	/app/data/saxs_computation/pc/1pcz/1pcz.dat