SAXSdb — 1a0a

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

PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)

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 A； UniProt 250–312 Chain B； UniProt 250–312	Fragment：DNA BINDING DOMAIN	;DNA (5'-D(CPTPCPAPCPAPCPGPTPGPGPGPAPCPTPAPG )-3') ; × 1 ;DNA (5'-D(CPTPAPGPTPCPCPCPAPCPGPTPGPTPGPAPG )-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 3.6；VAPOR DIFFUSION METHOD: DROP-0.4MM PROTEIN, 0.2MM DNA, 1% PEG6K, 20MM NACITRATE (PH3.6), RESERVOIR-1% PEG6K, 20MM NACITRATE(PH3.6), vapor diffusion	Resolution 2.80 Å R-free 0.284

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 1A0A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3W3X Crystal structure of Kap121p bound to Pho4p Deposited 2012-12-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 140–166（27 aa） Fragment：UNP residues 140-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.268
9D45 Cryo-EM structure of yeast Exportin Msn5 bound to cargo Pho4 and RanGTP Deposited 2024-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–200（200 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHO4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–63； UniProt 250–312 Author chain B； PDBConstruct 1–63； UniProt 250–312

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	1a0a
Deposition date deposition_date	1997-11-27
Structure title title	PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX
Keywords keywords	TRANSCRIPTION FACTOR, BASIC HELIX LOOP HELIX, COMPLEX (TRANSCRIPTION FACTOR-DNA), 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	20.28 Å
Radius of gyration Rg (electron density) rg_electron	19.58 Å
Forward intensity I(0) i0	18199200.00
Molecular weight molecular_weight	24602.0 kDa
Excluded volume excluded_volume	27466 Å³
Envelope volume envelope_volume	35764 Å³
Hydration-shell volume shell_volume	16227 Å³
Envelope diameter envelope_diameter	72.2 Å
Shell Rg shell_rg	24.77 Å
Envelope Rg envelope_rg	20.00 Å
Shape Rg shape_rg	19.55 Å
Total Rg total_rg	20.24 Å
Total atoms total_atoms	1687
Residues n_residues	160
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	68.2 Å
Rg (real space) rg_real	20.32 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.8200e+07
I(0) uncertainty (real space) i0_real_error	2.6040e+05
Rg (reciprocal space) rg_reciprocal	20.31 Å
I(0) (reciprocal space) i0_reciprocal	18200000.0000
Solution quality estimate total_estimate	0.8027
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.5 Å
Skewness Skewness skewness	0.360
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2712000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(CPTPCPAPCPAPCPGPTPGPGPGPAPCPTPAP*G )-3') ;
Molecular weight formula_weight	5212.4 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	1767

CTCACACGTGGGACTAG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPTPAPGPTPCPCPCPAPCPGPTPGPTPGPAP*G )-3') ;
Molecular weight formula_weight	5203.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CTAGTCCCACGTGTGAG

Entity 3 Entity 3 polymer

Description description	PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)
Molecular weight formula_weight	7104.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST

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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1a0aa_
Class class	a — All alpha proteins
Fold Fold fold	a.38 — HLH-like
Superfamily Superfamily superfamily	a.38.1 — HLH, helix-loop-helix DNA-binding domain
Family Family family	a.38.1.1 — HLH, helix-loop-helix DNA-binding domain

Domain ID domain_id	d1a0ab_
Class class	a — All alpha proteins
Fold Fold fold	a.38 — HLH-like
Superfamily Superfamily superfamily	a.38.1 — HLH, helix-loop-helix DNA-binding domain
Family Family family	a.38.1.1 — HLH, helix-loop-helix DNA-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	1a0aA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	1a0aB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	53.510 Å
Unit-cell length b length_b	68.300 Å
Unit-cell length c length_c	108.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2300
R_free r_free	0.2840

fit	/app/data/saxs_computation/a0/1a0a/1a0a.fit
pddf	/app/data/pr_computation/a0/1a0a/1a0a.pr.out
profile	/app/data/saxs_computation/a0/1a0a/1a0a.dat

PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX

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

PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 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)