SAXSdb — 5jlt

▼

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

Middle 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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 93–211	Not recorded	;DNA (5'-D(GPAPAPGPCPTPTPTPGPCPTPTPAPAPTPAPAPTPCPCPAPC)-3') ; × 1 ;DNA (5'-D(GPTPGPGPAPTPTPAPTPTPAPAPGPCPAPAPAPGPCPTPTPC)-3') ; × 1	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
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 93–211	Not recorded	;DNA (5'-D(GPAPAPGPCPTPTPTPGPCPTPTPAPAPTPAPAPTPCPCPAPC)-3') ; × 1 ;DNA (5'-D(GPTPGPGPAPTPTPAPTPTPAPAPGPCPAPAPAPGPCPTPTPC)-3') ; × 1	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
3	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 93–211 Chain D； UniProt 93–211	Not recorded	;DNA (5'-D(GPAPAPGPCPTPTPTPGPCPTPTPAPAPTPAPAPTPCPCPAPC)-3') ; × 1 ;DNA (5'-D(GPTPGPGPAPTPTPAPTPTPAPAPGPCPAPAPAPGPCPTPTPC)-3') ; × 1	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
4	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 93–211 Chain C； UniProt 93–211	Not recorded	;DNA (5'-D(GPAPAPGPCPTPTPTPGPCPTPTPAPAPTPAPAPTPCPCPAPC)-3') ; × 1 ;DNA (5'-D(GPTPGPGPAPTPTPAPTPTPAPAPGPCPAPAPAPGPCPTPTPC)-3') ; × 1	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

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 5JLT	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
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 10 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 7–125； UniProt 93–211 Author chain B； PDBConstruct 7–125； UniProt 93–211 Author chain C； PDBConstruct 7–125； UniProt 93–211 Author chain D； PDBConstruct 7–125； UniProt 93–211

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5jlt
Deposition date deposition_date	2016-04-27
Structure title title	The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif
Keywords keywords	;MotA, dsDNA, "Double wing", DNA binding motif, VIRAL PROTEIN-DNA complex ;; VIRAL PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.80 Å
Radius of gyration Rg (electron density) rg_electron	35.06 Å
Forward intensity I(0) i0	141766000.00
Molecular weight molecular_weight	77802.0 kDa
Excluded volume excluded_volume	89966 Å³
Envelope volume envelope_volume	134080 Å³
Hydration-shell volume shell_volume	35144 Å³
Envelope diameter envelope_diameter	125.7 Å
Shell Rg shell_rg	37.48 Å
Envelope Rg envelope_rg	34.83 Å
Shape Rg shape_rg	35.05 Å
Total Rg total_rg	35.23 Å
Total atoms total_atoms	5342
Residues n_residues	526
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	117.2 Å
Rg (real space) rg_real	35.04 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	1.4180e+08
I(0) uncertainty (real space) i0_real_error	2.7700e+06
Rg (reciprocal space) rg_reciprocal	34.89 Å
I(0) (reciprocal space) i0_reciprocal	141700000.0000
Solution quality estimate total_estimate	0.8530
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.9 Å
Skewness Skewness skewness	0.493
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8527000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.878; Smooth: 0.652

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Middle transcription regulatory protein motA
Molecular weight formula_weight	14548.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5739

EGDIHMELLKKRATRKAREITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL

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

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPAPAPGPCPTPTPTPGPCPTPTPAPAPTPAPAPTPCPCPAPC)-3') ;
Molecular weight formula_weight	6710.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,H

GAAGCTTTGCTTAATAATCCAC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPTPGPGPAPTPTPAPTPTPAPAPGPCPAPAPAPGPCPTPTPC)-3') ;
Molecular weight formula_weight	6790.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,G

GTGGATTATTAAGCAAAGCTTC

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	387

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5jltA00
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	5jltB00
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	5jltC00
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	5jltD00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	72.270 Å
Unit-cell length b length_b	72.270 Å
Unit-cell length c length_c	279.369 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	24

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

Resolution resolution	2.955 Å
Low-resolution limit resolution_low	62.588 Å
R factor r_factor	0.2208
R_work r_work	0.2195
R_free r_free	0.2446

fit	/app/data/saxs_computation/jl/5jlt/5jlt.fit
pddf	/app/data/pr_computation/jl/5jlt/5jlt.pr.out
profile	/app/data/saxs_computation/jl/5jlt/5jlt.dat

The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif

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

Middle 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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)