SAXSdb — 1kaf

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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 105–211	Fragment：DNA binding domain residues 105-211	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 105–211	Fragment：DNA binding domain residues 105-211	No other associated polymer	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 105–211	Fragment：DNA binding domain residues 105-211	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 105–211	Fragment：DNA binding domain residues 105-211	No other associated polymer	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 105–211	Fragment：DNA binding domain residues 105-211	No other associated polymer	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 105–211	Fragment：DNA binding domain residues 105-211	No other associated polymer	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

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 1KAF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BJA ACTIVATION DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA Deposited 1998-06-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–96（95 aa） Fragment：N-TERMINAL ACTIVATION DOMAIN	Not recorded	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
1BJA ACTIVATION DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA Deposited 1998-06-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–96（95 aa） Fragment：N-TERMINAL ACTIVATION DOMAIN	Not recorded	No recorded non-water small molecule	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
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
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 8 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 2–108； UniProt 105–211 Author chain B； PDBConstruct 2–108； UniProt 105–211 Author chain C； PDBConstruct 2–108； UniProt 105–211 Author chain D； PDBConstruct 2–108； UniProt 105–211 Author chain E； PDBConstruct 2–108； UniProt 105–211 Author chain F； PDBConstruct 2–108； UniProt 105–211

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	1kaf
Deposition date deposition_date	2001-11-01
Structure title title	DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211)
Keywords keywords	Escherichia coli; X-ray crystallography; protein-DNA interactions; structural genomics; eubacterial promoters., TRANSCRIPTION; TRANSCRIPTION
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	32.58 Å
Radius of gyration Rg (electron density) rg_electron	32.52 Å
Forward intensity I(0) i0	86449500.00
Molecular weight molecular_weight	73616.0 kDa
Excluded volume excluded_volume	92338 Å³
Envelope volume envelope_volume	124830 Å³
Hydration-shell volume shell_volume	33841 Å³
Envelope diameter envelope_diameter	110.7 Å
Shell Rg shell_rg	37.45 Å
Envelope Rg envelope_rg	31.94 Å
Shape Rg shape_rg	32.52 Å
Total Rg total_rg	32.96 Å
Total atoms total_atoms	5142
Residues n_residues	635
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	107.8 Å
Rg (real space) rg_real	32.76 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	8.6450e+07
I(0) uncertainty (real space) i0_real_error	1.3010e+06
Rg (reciprocal space) rg_reciprocal	32.69 Å
I(0) (reciprocal space) i0_reciprocal	86440000.0000
Solution quality estimate total_estimate	0.8740
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.4 Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.438
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12010000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.859

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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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1kafa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.199 — MotA C-terminal domain-like
Superfamily Superfamily superfamily	d.199.1 — DNA-binding C-terminal domain of the transcription factor MotA
Family Family family	d.199.1.1 — DNA-binding C-terminal domain of the transcription factor MotA

Domain ID domain_id	d1kafb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.199 — MotA C-terminal domain-like
Superfamily Superfamily superfamily	d.199.1 — DNA-binding C-terminal domain of the transcription factor MotA
Family Family family	d.199.1.1 — DNA-binding C-terminal domain of the transcription factor MotA

Domain ID domain_id	d1kafc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.199 — MotA C-terminal domain-like
Superfamily Superfamily superfamily	d.199.1 — DNA-binding C-terminal domain of the transcription factor MotA
Family Family family	d.199.1.1 — DNA-binding C-terminal domain of the transcription factor MotA

Domain ID domain_id	d1kafd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.199 — MotA C-terminal domain-like
Superfamily Superfamily superfamily	d.199.1 — DNA-binding C-terminal domain of the transcription factor MotA
Family Family family	d.199.1.1 — DNA-binding C-terminal domain of the transcription factor MotA

Domain ID domain_id	d1kafe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.199 — MotA C-terminal domain-like
Superfamily Superfamily superfamily	d.199.1 — DNA-binding C-terminal domain of the transcription factor MotA
Family Family family	d.199.1.1 — DNA-binding C-terminal domain of the transcription factor MotA

Domain ID domain_id	d1kaff_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.199 — MotA C-terminal domain-like
Superfamily Superfamily superfamily	d.199.1 — DNA-binding C-terminal domain of the transcription factor MotA
Family Family family	d.199.1.1 — DNA-binding C-terminal domain of the transcription factor MotA

CATH v4.4 (6 domains)

Domain ID domain_id	1kafA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	20 — Transcription regulator MotA, C-terminal domain

Domain ID domain_id	1kafB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	20 — Transcription regulator MotA, C-terminal domain

Domain ID domain_id	1kafC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	20 — Transcription regulator MotA, C-terminal domain

Domain ID domain_id	1kafD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	20 — Transcription regulator MotA, C-terminal domain

Domain ID domain_id	1kafE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	20 — Transcription regulator MotA, C-terminal domain

Domain ID domain_id	1kafF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	20 — Transcription regulator MotA, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	31.284 Å
Unit-cell length b length_b	54.733 Å
Unit-cell length c length_c	91.445 Å
Unit-cell angle α angle_alpha	94.77 °
Unit-cell angle β angle_beta	91.10 °
Unit-cell angle γ angle_gamma	95.61 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2260
R_free r_free	0.2580

Description description	Transcription regulatory protein MOTA
Molecular weight formula_weight	12538.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5785

DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211)

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

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	643

fit	/app/data/saxs_computation/ka/1kaf/1kaf.fit
pddf	/app/data/pr_computation/ka/1kaf/1kaf.pr.out
profile	/app/data/saxs_computation/ka/1kaf/1kaf.dat