SAXSdb — 1bja

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

TRANSCRIPTION REGULATORY PROTEIN MOTA

Enterobacteria phage T4

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 2–96	Fragment：N-TERMINAL ACTIVATION DOMAIN	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 60% SATURATED AMMONIUM SULPHATE, 100 MM BIS-TRIS PROPANE, PH 8.0 - 9.0, pH 8.5	Resolution 2.19 Å R-free 0.291
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–96	Fragment：N-TERMINAL ACTIVATION DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 60% SATURATED AMMONIUM SULPHATE, 100 MM BIS-TRIS PROPANE, PH 8.0 - 9.0, pH 8.5	Resolution 2.19 Å R-free 0.291

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 1BJA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I1S SOLUTION STRUCTURE OF THE TRANSCRIPTIONAL ACTIVATION DOMAIN OF THE BACTERIOPHAGE T4 PROTEIN MOTA Deposited 2001-02-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-96	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；301 K；Ionic strength (raw mmCIF value) 200 mM potassium phosphate；Pressure ambient NMR measurement conditions pH 6.5；301 K；Ionic strength (raw mmCIF value) 200 mM potassium phosphate；Pressure ambient NMR sample composition 2mM MotNF U-15N \| 200 mM potassium phosphate buffer, pH 6.5; 90% H2O, 10% D2O NMR sample composition 2mM MotNF U-13C,15N \| 200 mM potassium phosphate buffer, pH 6.5; 90% H2O, 10% D2O	Resolution not provided
1KAF DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211) Deposited 2001-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 105–211（107 aa） Fragment：DNA binding domain residues 105-211	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.258
1KAF DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211) Deposited 2001-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 105–211（107 aa） Fragment：DNA binding domain residues 105-211	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.258
1KAF DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211) Deposited 2001-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 105–211（107 aa） Fragment：DNA binding domain residues 105-211	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.258
1KAF DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211) Deposited 2001-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 105–211（107 aa） Fragment：DNA binding domain residues 105-211	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.258
1KAF DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211) Deposited 2001-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 105–211（107 aa） Fragment：DNA binding domain residues 105-211	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.258
1KAF DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211) Deposited 2001-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 105–211（107 aa） Fragment：DNA binding domain residues 105-211	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.258
5JLT The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif Deposited 2016-04-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 93–211（119 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；23% PEG 8K, 0.1 M Na Acetate, 0.1 M NaCacodylate, pH 6.5, and 3% glycerol	Resolution 2.96 Å R-free 0.245
5JLT The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif Deposited 2016-04-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 93–211（119 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；23% PEG 8K, 0.1 M Na Acetate, 0.1 M NaCacodylate, pH 6.5, and 3% glycerol	Resolution 2.96 Å R-free 0.245
5JLT The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif Deposited 2016-04-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 93–211（119 aa） Chain D 93–211（119 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；23% PEG 8K, 0.1 M Na Acetate, 0.1 M NaCacodylate, pH 6.5, and 3% glycerol	Resolution 2.96 Å R-free 0.245
5JLT The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif Deposited 2016-04-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain B 93–211（119 aa） Chain C 93–211（119 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；23% PEG 8K, 0.1 M Na Acetate, 0.1 M NaCacodylate, pH 6.5, and 3% glycerol	Resolution 2.96 Å R-free 0.245
6K4Y CryoEM structure of sigma appropriation complex Deposited 2019-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain M 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.79 Å

4 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MOTA_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 2–96 Author chain B； PDBConstruct 1–95； UniProt 2–96

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	1bja
Deposition date deposition_date	1998-06-23
Structure title title	ACTIVATION DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA
Keywords keywords	ACTIVATION DOMAIN, PHAGE T4, MIDDLE MODE TRANSCRIPTION, ALPHA HELICAL STRUCTURE, TRANSCRIPTION REGULATION; ACTIVATION DOMAIN
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	21.54 Å
Radius of gyration Rg (electron density) rg_electron	20.96 Å
Forward intensity I(0) i0	6985090.00
Molecular weight molecular_weight	20299.0 kDa
Excluded volume excluded_volume	25801 Å³
Envelope volume envelope_volume	30801 Å³
Hydration-shell volume shell_volume	13575 Å³
Envelope diameter envelope_diameter	69.2 Å
Shell Rg shell_rg	25.16 Å
Envelope Rg envelope_rg	21.04 Å
Shape Rg shape_rg	20.94 Å
Total Rg total_rg	21.68 Å
Total atoms total_atoms	1427
Residues n_residues	190
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	70.5 Å
Rg (real space) rg_real	21.76 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	6.9850e+06
I(0) uncertainty (real space) i0_real_error	9.7800e+04
Rg (reciprocal space) rg_reciprocal	21.72 Å
I(0) (reciprocal space) i0_reciprocal	6985000.0000
Solution quality estimate total_estimate	0.8115
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	-0.665
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2234000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.657; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.614; Smooth: 0.962

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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	TRANSCRIPTION REGULATORY PROTEIN MOTA
Molecular weight formula_weight	10114.6 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	1487

SKVTYIIKASNDVLNEKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISNAATLYAQENAPELLK

来源 Source

来源生物 organism	Enterobacteria phage T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bjaa_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.9 — Transcription factor MotA, activation domain

Domain ID domain_id	d1bjab_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.9 — Transcription factor MotA, activation domain

CATH v4.4 (2 domains)

Domain ID domain_id	1bjaA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1bjaB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	46.700 Å
Unit-cell length b length_b	46.700 Å
Unit-cell length c length_c	139.600 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2910

fit	/app/data/saxs_computation/bj/1bja/1bja.fit
pddf	/app/data/pr_computation/bj/1bja/1bja.pr.out
profile	/app/data/saxs_computation/bj/1bja/1bja.dat

ACTIVATION DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA

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

TRANSCRIPTION REGULATORY PROTEIN MOTA

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