SAXSdb — 1apl

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

PROTEIN (MAT-ALPHA2 HOMEODOMAIN)

Saccharomyces cerevisiae

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 Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 128–210 Chain D； UniProt 128–210	Not recorded	;DNA (5'-D(APCPAPTPGPTPAPAPTPTPCPAPTPTPTPAPC PAPCPGPC)-3') ; × 1 ;DNA (5'-D(TPGPCPGPTPGPTPAPAPAPTPGPAPAPTPTPA PCPAPTPG)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.50, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å

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 1APL	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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 128–210（83 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
1MNM YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE Deposited 1997-11-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 103–189（87 aa） Fragment：RESIDUES 113 - 189 Chain D 103–189（87 aa） Fragment：RESIDUES 113 - 189	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.50	Resolution 2.25 Å R-free 0.285
1YRN CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA Deposited 1995-11-02	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 B 128–210（83 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MTAL2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–83； UniProt 128–210 Author chain D； 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	1apl
Deposition date deposition_date	1993-10-04
Structure title title	CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS
Keywords keywords	PROTEIN-DNA COMPLEX, DOUBLE HELIX, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/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	23.19 Å
Radius of gyration Rg (electron density) rg_electron	23.25 Å
Forward intensity I(0) i0	20291000.00
Molecular weight molecular_weight	26148.0 kDa
Excluded volume excluded_volume	29006 Å³
Envelope volume envelope_volume	39672 Å³
Hydration-shell volume shell_volume	15435 Å³
Envelope diameter envelope_diameter	76.3 Å
Shell Rg shell_rg	28.27 Å
Envelope Rg envelope_rg	22.94 Å
Shape Rg shape_rg	23.24 Å
Total Rg total_rg	23.77 Å
Total atoms total_atoms	1791
Residues n_residues	159
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	80.9 Å
Rg (real space) rg_real	23.37 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	2.0290e+07
I(0) uncertainty (real space) i0_real_error	3.0030e+05
Rg (reciprocal space) rg_reciprocal	23.33 Å
I(0) (reciprocal space) i0_reciprocal	20290000.0000
Solution quality estimate total_estimate	0.7122
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.9 Å
Skewness Skewness skewness	0.416
Kurtosis Kurtosis kurtosis	-0.691
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1800000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.579; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.547; Smooth: 0.000

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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	;DNA (5'-D(APCPAPTPGPTPAPAPTPTPCPAPTPTPTPAPC PAPCPGP*C)-3') ;
Molecular weight formula_weight	6381.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	1791

ACATGTAATTCATTTACACGC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPGPCPGPTPGPTPAPAPAPTPGPAPAPTPTPA PCPAPTP*G)-3') ;
Molecular weight formula_weight	6501.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

TGCGTGTAAATGAATTACATG

Entity 3 Entity 3 polymer

Description description	PROTEIN (MAT-ALPHA2 HOMEODOMAIN)
Molecular weight formula_weight	9773.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPLAKKKE

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

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1aplc_
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	d1apld_
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	1aplC00
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	1aplD00
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 (2)

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Unit-cell length a length_a	60.780 Å
Unit-cell length b length_b	39.930 Å
Unit-cell length c length_c	68.790 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	—

fit	/app/data/saxs_computation/ap/1apl/1apl.fit
pddf	/app/data/pr_computation/ap/1apl/1apl.pr.out
profile	/app/data/saxs_computation/ap/1apl/1apl.dat

CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS

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

PROTEIN (MAT-ALPHA2 HOMEODOMAIN)

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)