SAXSdb — 1dh3

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

TRANSCRIPTION FACTOR CREB

Mus musculus

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 201–255 Chain C； UniProt 201–255	Fragment：RESIDUES 201-255	;DNA (5'-D(CPCPTPTPGPGPCPTPGPAPCPGPTPCPAPGPCPCPAPAP*G)-3') ; × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；PEG 8000, MGCL2, (NH4)2SO4, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.K	Resolution 3.00 Å R-free 0.280

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	CREB1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–55； UniProt 201–255 Author chain C； PDBConstruct 1–55； UniProt 201–255

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	1dh3
Deposition date deposition_date	1999-11-27
Structure title title	CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING
Keywords keywords	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	24.75 Å
Radius of gyration Rg (electron density) rg_electron	25.74 Å
Forward intensity I(0) i0	20634100.00
Molecular weight molecular_weight	26197.0 kDa
Excluded volume excluded_volume	29182 Å³
Envelope volume envelope_volume	42349 Å³
Hydration-shell volume shell_volume	16049 Å³
Envelope diameter envelope_diameter	88.7 Å
Shell Rg shell_rg	28.41 Å
Envelope Rg envelope_rg	26.21 Å
Shape Rg shape_rg	25.76 Å
Total Rg total_rg	25.96 Å
Total atoms total_atoms	1787
Residues n_residues	152
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	84.8 Å
Rg (real space) rg_real	25.11 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	2.0630e+07
I(0) uncertainty (real space) i0_real_error	2.8940e+05
Rg (reciprocal space) rg_reciprocal	25.03 Å
I(0) (reciprocal space) i0_reciprocal	20630000.0000
Solution quality estimate total_estimate	0.8171
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	0.531
Kurtosis Kurtosis kurtosis	-0.417
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1146000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.423; Smooth: 0.919

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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(CPCPTPTPGPGPCPTPGPAPCPGPTPCPAPGPCPCPAPAP*G)-3') ;
Molecular weight formula_weight	6424.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,D
Atom count atom_count	1804

CCTTGGCTGACGTCAGCCAAG

Entity 2 Entity 2 polymer

Description description	TRANSCRIPTION FACTOR CREB
Molecular weight formula_weight	6686.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

KREVRLMKNREAARESRRKKKEYVKSLENRVAVLENQNKTLIEELKALKDLYSHK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dh3a_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1dh3c_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

CATH v4.4 (2 domains)

Domain ID domain_id	1dh3A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	1dh3C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

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8. Citations (1)

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Unit-cell length a length_a	110.610 Å
Unit-cell length b length_b	49.320 Å
Unit-cell length c length_c	79.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2180
R_work r_work	0.2230
R_free r_free	0.2800

fit	/app/data/saxs_computation/dh/1dh3/1dh3.fit
pddf	/app/data/pr_computation/dh/1dh3/1dh3.pr.out
profile	/app/data/saxs_computation/dh/1dh3/1dh3.dat

CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING

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

TRANSCRIPTION FACTOR CREB

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

来源 Source

Entity 3 Entity 3 non-polymer

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)