6mg3

V285A Mutant of the C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence

Method: X-RAY DIFFRACTION Dmax: 99.6 Å Quality: REASONABLE

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

CCAAT/enhancer-binding protein beta

Homo sapiens

UniProt P17676

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 246–321 Chain B; UniProt 246–321 Mutation:V285A 16-bp methylated oligonucleotide × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;292 K;0.1 M sodium acetate trihydrate pH 7.0, 12% (w/v) polyethylene glycol 3350 Resolution 2.05 Å R-free 0.249

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.

15 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CEBPB_HUMAN
Isoform P17676-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–78; UniProt 246–321 Author chain B; PDBConstruct 3–78; UniProt 246–321

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6mg3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6mg3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6mg3
Deposition date deposition_date2018-09-12
Structure title titleV285A Mutant of the C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence
Keywords keywordsbZIP Transciption Factor DNA Methylation CpA methylation PROTEIN-DNA COMPLEX, TRANSCRIPTION, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.62
Radius of gyration Rg (electron density) rg_electron27.69
Forward intensity I(0) i017711200.00
Molecular weight molecular_weight25410.0 kDa
Excluded volume excluded_volume28931 ų
Envelope volume envelope_volume41490 ų
Hydration-shell volume shell_volume14961 ų
Envelope diameter envelope_diameter102.7
Shell Rg shell_rg29.03
Envelope Rg envelope_rg28.85
Shape Rg shape_rg27.77
Total Rg total_rg27.63
Total atoms total_atoms1747
Residues n_residues160
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax99.6
Rg (real space) rg_real26.25
Rg uncertainty (real space) rg_real_error1.59
I(0) (real space) i0_real1.7710e+07
I(0) uncertainty (real space) i0_real_error3.1910e+05
Rg (reciprocal space) rg_reciprocal26.06
I(0) (reciprocal space) i0_reciprocal17710000.0000
Solution quality estimate total_estimate0.6749
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.3
Skewness Skewness skewness0.781
Kurtosis Kurtosis kurtosis-0.068
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1261000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.244; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.063; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6mg3A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily170
Domain ID domain_id6mg3B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily170

8. Citations (1)

9. Files and Curves (10)