SAXSdb — 1zk9

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

Transcription factor RelB

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 277–378	Fragment：dimerization domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 8000, ammonium sulfate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.18 Å R-free 0.218

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 1ZK9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZKA NF-kB RelB forms an intertwined homodimer, Y300S mutant Deposited 2005-05-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 277–378（102 aa） Fragment：dimerization domain	Mutation：Y300S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 8000,AS, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.231
2V2T X-ray structure of a NF-kB p50-RelB-DNA complex Deposited 2007-06-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 91–378（288 aa） Fragment：RESIDUES 91-378	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；5% PEG3350 100 MM NACITRATE 1MM SPERMINE 5MM DTT, pH 7	Resolution 3.05 Å R-free 0.276
3JSS Crystal structure of a mutant RelB dimerization domain Deposited 2009-09-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Mutation：V314R, A324G, F358Q, L362K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG800, 0.1M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.259
3JUZ Crystal structure of a mutant of RelB dimerization domain(M5) Deposited 2009-09-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Mutation：V314R, A324G, F358Q, L362K, N287D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20 % PEG8000, 0.1 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.51 Å R-free 0.226
3JV0 Crystal structure of a mutant of RelB dimerization domain(M6) Deposited 2009-09-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Mutation：V314R, A324G, F358Q, L362K, N287D, I335F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20 % PEG8000, 0.1 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.65 Å R-free 0.258
3JV4 Crystal structure of the dimerization domains p50 and RelB Deposited 2009-09-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG8000, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.15 Å R-free 0.280
3JV4 Crystal structure of the dimerization domains p50 and RelB Deposited 2009-09-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG8000, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.15 Å R-free 0.280
3JV4 Crystal structure of the dimerization domains p50 and RelB Deposited 2009-09-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG8000, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.15 Å R-free 0.280
3JV6 Crystal structure of the dimerization domains p52 and RelB Deposited 2009-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 8000, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.78 Å R-free 0.248
3JV6 Crystal structure of the dimerization domains p52 and RelB Deposited 2009-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 8000, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.78 Å R-free 0.248
3JV6 Crystal structure of the dimerization domains p52 and RelB Deposited 2009-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 278–378（101 aa） Fragment：dimerization domain (UNP residues 278-378)	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 8000, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.78 Å R-free 0.248
4JGM Crystal structure of RelB double mutants: Y300F/I335V Deposited 2013-03-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 277–378（102 aa） Fragment：Dimerization domain	Mutation：Y300F, I335V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；30% PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.292
4JHB Crystal structure of RelB double mutants: Y300F/I335F Deposited 2013-03-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 277–378（102 aa） Fragment：Dimerization domain	Mutation：Y300F, I335F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；30% PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.44 Å R-free 0.226

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RELB_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–110； UniProt 277–378

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	1zk9
Deposition date deposition_date	2005-05-02
Structure title title	NF-kB RelB forms an intertwined homodimer
Keywords keywords	NF-kB, Transcription factors, intertwined dimer, TRANSCRIPTION; TRANSCRIPTION
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	20.44 Å
Radius of gyration Rg (electron density) rg_electron	19.63 Å
Forward intensity I(0) i0	3237530.00
Molecular weight molecular_weight	12365.0 kDa
Excluded volume excluded_volume	15448 Å³
Envelope volume envelope_volume	24284 Å³
Hydration-shell volume shell_volume	11909 Å³
Envelope diameter envelope_diameter	61.1 Å
Shell Rg shell_rg	22.79 Å
Envelope Rg envelope_rg	18.85 Å
Shape Rg shape_rg	19.62 Å
Total Rg total_rg	20.34 Å
Total atoms total_atoms	869
Residues n_residues	110
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	63.1 Å
Rg (real space) rg_real	20.47 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	3.2380e+06
I(0) uncertainty (real space) i0_real_error	4.2670e+04
Rg (reciprocal space) rg_reciprocal	20.47 Å
I(0) (reciprocal space) i0_reciprocal	3238000.0000
Solution quality estimate total_estimate	0.9079
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.274
Kurtosis Kurtosis kurtosis	-0.577
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	287800.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1zk9a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain

Domain ID domain_id	d1zk9a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1zk9A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	69.200 Å
Unit-cell length b length_b	69.200 Å
Unit-cell length c length_c	64.740 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	14.980 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2180

Description description	Transcription factor RelB
Molecular weight formula_weight	12400.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	972

NF-kB RelB forms an intertwined homodimer

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

Transcription factor RelB

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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 BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

fit	/app/data/saxs_computation/zk/1zk9/1zk9.fit
pddf	/app/data/pr_computation/zk/1zk9/1zk9.pr.out
profile	/app/data/saxs_computation/zk/1zk9/1zk9.dat