SAXSdb — 1le8

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

MATING-TYPE PROTEIN A-1

OrganismNot specified

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 74–126	Fragment：residues 74-126	5'-D(APCPAPTPGPTPAPAPAPAPAPTPTPTPAPCPAPTPCPA)-3' × 1 5'-D(TPTPGPAPTPGPTPAPAPAPTPTPTPTPTPAPCPAPTPG)-3' × 1 Mating-type protein alpha-2 × 1 （Q6B184）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10% PEG400, 8 mM Co(NH3)6Cl3, 10 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.299

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 1LE8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AKH MAT A1/ALPHA2/DNA TERNARY COMPLEX Deposited 1997-05-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 66–126（61 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；100MM HEPES PH 7.0, 20MM CACL2, 5MM [CO(NH3)6]CL3., VAPOR DIFFUSION, HANGING DROP, temperature 295.00K	Resolution 2.50 Å R-free 0.302
1F43 SOLUTION STRUCTURE OF THE MATA1 HOMEODOMAIN Deposited 2000-06-07	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 66–126（61 aa） Fragment：HOMEODOMAIN, C-TERMINAL DOMAIN (66-126)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient NMR sample composition 1.5 mM MATa1(66-126) U-15N,13C 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5 mM MATa1 (66-126) U-15N 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5 mM MATa1 (66-126) 25 mM deuterated acetate, pH 4.5, 100 mM KCl, 0.01% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1MH3 maltose binding-a1 homeodomain protein chimera, crystal form I Deposited 2002-08-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–126（50 aa）	Mutation：E359A, K362A, D363A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；amonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.262
1MH4 maltose binding-a1 homeodomain protein chimera, crystal form II Deposited 2002-08-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–126（50 aa）	Mutation：E359A, K362A, D363A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.293
1YRN CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA Deposited 1995-11-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 66–126（61 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.298

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MATA1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 74–126

Mating-type protein alpha-2

Saccharomyces cerevisiae

UniProt Q6B184

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 128–210	Fragment：residues 128-210 Mutation：S181A, N182A, R185A	5'-D(APCPAPTPGPTPAPAPAPAPAPTPTPTPAPCPAPTPCPA)-3' × 1 5'-D(TPTPGPAPTPGPTPAPAPAPTPTPTPTPTPAPCPAPTPG)-3' × 1 MATING-TYPE PROTEIN A-1 × 1 （P01366）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10% PEG400, 8 mM Co(NH3)6Cl3, 10 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.299

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	MATA2_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–83； UniProt 128–210

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	1le8
Deposition date deposition_date	2002-04-09
Structure title title	Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex
Keywords keywords	MATalpha2, isothermal titration calorimetry, protein-DNA complex, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	20.55 Å
Radius of gyration Rg (electron density) rg_electron	19.80 Å
Forward intensity I(0) i0	19686400.00
Molecular weight molecular_weight	26356.0 kDa
Excluded volume excluded_volume	29693 Å³
Envelope volume envelope_volume	38688 Å³
Hydration-shell volume shell_volume	16864 Å³
Envelope diameter envelope_diameter	65.2 Å
Shell Rg shell_rg	25.14 Å
Envelope Rg envelope_rg	19.74 Å
Shape Rg shape_rg	19.74 Å
Total Rg total_rg	20.52 Å
Total atoms total_atoms	1807
Residues n_residues	167
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	67.3 Å
Rg (real space) rg_real	20.55 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.9690e+07
I(0) uncertainty (real space) i0_real_error	2.2240e+05
Rg (reciprocal space) rg_reciprocal	20.55 Å
I(0) (reciprocal space) i0_reciprocal	19690000.0000
Solution quality estimate total_estimate	0.7548
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.290
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2547000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 0.387; Positv: 1.000; Valcen: 0.970; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	5'-D(APCPAPTPGPTPAPAPAPAPAPTPTPTPAPCPAPTPCPA)-3'
Molecular weight formula_weight	6109.0 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	1909

ACATGTAAAAATTTACATCA

Entity 2 Entity 2 polymer

Description description	5'-D(TPTPGPAPTPGPTPAPAPAPTPTPTPTPTPAPCPAPTPG)-3'
Molecular weight formula_weight	6153.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTGATGTAAATTTTTACATG

Entity 3 Entity 3 polymer

Description description	MATING-TYPE PROTEIN A-1
Molecular weight formula_weight	6277.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK

Entity 4 Entity 4 polymer

Description description	Mating-type protein alpha-2
Molecular weight formula_weight	9628.2 kDa
Mutation mutation	S181A, N182A, R185A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAPELADLLSGEPLAKKKE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1le8a_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.1 — Homeodomain

Domain ID domain_id	d1le8b_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.1 — Homeodomain

CATH v4.4 (2 domains)

Domain ID domain_id	1le8A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1le8B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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8. Citations (1)

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Unit-cell length a length_a	54.170 Å
Unit-cell length b length_b	54.170 Å
Unit-cell length c length_c	164.230 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	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	24.280 Å
R factor r_factor	—
R_work r_work	0.2560
R_free r_free	0.2990

fit	/app/data/saxs_computation/le/1le8/1le8.fit
pddf	/app/data/pr_computation/le/1le8/1le8.pr.out
profile	/app/data/saxs_computation/le/1le8/1le8.dat

Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex

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

MATING-TYPE PROTEIN A-1

State in the Current Structure

Other States of the Same Protein in the Database

Mating-type protein alpha-2

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

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)