SAXSdb — 1au7

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

PROTEIN PIT-1

Rattus norvegicus

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 130–273 Chain B； UniProt 130–273	Mutation：E5G, I6M	CONSENSUS DNA 25-MER × 1 ;DNA (5'-D(CPTPTPCPCPTPCPAPTPGPTPAPTPAPTPAPC PAPTPGPAPGP* GP*A)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；A 28 BP DNA DUPLEX (10MG/ML) WAS ADDED TO THE PROTEIN IN A 1:2 MOLAR RATIO. CRYSTALS WERE GROWN BY VAPOR DIFFUSION USING HANGING DROPS OF 1 UL. OF PROTEIN/DNA SOLUTION MIXED 1 UL. OF RESERVOIR SOLUTION. THE BEST CRYSTALS WERE OBTAINED WITH RESERVOIRS CONTAINING 400-600 MM PHOSPHORIC ACID ADJUSTED TO PH 4.0 - 4.3 WITH TRIETHYLAMINE., pH 4.00, vapor diffusion - hanging drop	Resolution 2.30 Å R-free 0.302

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	PIT1_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 130–273 Author chain B； PDBConstruct 1–146； UniProt 130–273

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	1au7
Deposition date deposition_date	1997-09-12
Structure title title	PIT-1 MUTANT/DNA COMPLEX
Keywords keywords	COMPLEX (DNA-BINDING PROTEIN-DNA), PITUITARY, CPHD, POU DOMAIN, TRANSCRIPTION FACTOR, 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	24.44 Å
Radius of gyration Rg (electron density) rg_electron	23.60 Å
Forward intensity I(0) i0	50926500.00
Molecular weight molecular_weight	44981.0 kDa
Excluded volume excluded_volume	51867 Å³
Envelope volume envelope_volume	69234 Å³
Hydration-shell volume shell_volume	24784 Å³
Envelope diameter envelope_diameter	90.0 Å
Shell Rg shell_rg	30.13 Å
Envelope Rg envelope_rg	23.76 Å
Shape Rg shape_rg	23.57 Å
Total Rg total_rg	24.31 Å
Total atoms total_atoms	3741
Residues n_residues	307
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	85.9 Å
Rg (real space) rg_real	24.48 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	5.0930e+07
I(0) uncertainty (real space) i0_real_error	7.6820e+05
Rg (reciprocal space) rg_reciprocal	24.47 Å
I(0) (reciprocal space) i0_reciprocal	50930000.0000
Solution quality estimate total_estimate	0.8618
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.405
Kurtosis Kurtosis kurtosis	-0.182
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7879000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.876; Smooth: 0.989

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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	CONSENSUS DNA 25-MER
Molecular weight formula_weight	7722.0 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	4269

TCCTCATGTATATACATGAGGAAGG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPTPTPCPCPTPCPAPTPGPTPAPTPAPTPAPC PAPTPGPAPGP* GP*A)-3') ;
Molecular weight formula_weight	7343.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CTTCCTCATGTATATACATGAGGA

Entity 3 Entity 3 polymer

Description description	PROTEIN PIT-1
Molecular weight formula_weight	17003.6 kDa
Mutation mutation	E5G, I6M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GMRALEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1au7a1
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	d1au7a2
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.1 — POU-specific domain

Domain ID domain_id	d1au7b1
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	d1au7b2
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.1 — POU-specific domain

CATH v4.4 (4 domains)

Domain ID domain_id	1au7A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1au7A02
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	1au7B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	1au7B02
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	42.500 Å
Unit-cell length b length_b	50.100 Å
Unit-cell length c length_c	55.800 Å
Unit-cell angle α angle_alpha	76.70 °
Unit-cell angle β angle_beta	79.30 °
Unit-cell angle γ angle_gamma	67.20 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.2300
R_free r_free	0.3020

fit	/app/data/saxs_computation/au/1au7/1au7.fit
pddf	/app/data/pr_computation/au/1au7/1au7.pr.out
profile	/app/data/saxs_computation/au/1au7/1au7.dat

PIT-1 MUTANT/DNA COMPLEX

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

PROTEIN PIT-1

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)