4qc3

Crystal structure of human BAZ2B bromodomain in complex with a diacetylated histone 4 peptide (H4K8acK12ac)

Method: X-RAY DIFFRACTION Dmax: 77.3 Å Quality: REASONABLE

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

Bromodomain adjacent to zinc finger domain protein 2B

Homo sapiens

UniProt Q9UIF8

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2062–2166 Fragment:unp residues 2062-2166 diacetylated histone 4 peptide (H4K8acK12ac) × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;18% PEG 8000, 0.2M calcium acetate, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 1.60 Å R-free 0.187
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2062–2166 Fragment:unp residues 2062-2166 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;18% PEG 8000, 0.2M calcium acetate, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 1.60 Å R-free 0.187

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.

263 other PDB entries and 270 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BAZ2B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–107; UniProt 2062–2166 Author chain B; PDBConstruct 3–107; UniProt 2062–2166

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 4qc3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qc3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qc3
Deposition date deposition_date2014-05-09
Structure title titleCrystal structure of human BAZ2B bromodomain in complex with a diacetylated histone 4 peptide (H4K8acK12ac)
Keywords keywords;Bromodomain adjacent to zinc finger domain protein 2B, hWALp4, KIAA1476, transcriptional regulation, Structural Genomics Consortium, SGC, TRANSCRIPTION ;; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.77
Radius of gyration Rg (electron density) rg_electron23.30
Forward intensity I(0) i011370800.00
Molecular weight molecular_weight25643.0 kDa
Excluded volume excluded_volume32184 ų
Envelope volume envelope_volume39687 ų
Hydration-shell volume shell_volume15584 ų
Envelope diameter envelope_diameter81.3
Shell Rg shell_rg27.92
Envelope Rg envelope_rg23.22
Shape Rg shape_rg23.26
Total Rg total_rg24.08
Total atoms total_atoms1799
Residues n_residues219
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 dmax77.3
Rg (real space) rg_real24.00
Rg uncertainty (real space) rg_real_error0.74
I(0) (real space) i0_real1.1370e+07
I(0) uncertainty (real space) i0_real_error1.8930e+05
Rg (reciprocal space) rg_reciprocal23.95
I(0) (reciprocal space) i0_reciprocal11370000.0000
Solution quality estimate total_estimate0.7330
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.1
Skewness Skewness skewness0.421
Kurtosis Kurtosis kurtosis-0.708
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4187000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.673; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.526; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4qc3a1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.2 — Bromodomain
Family Family familya.29.2.0 — automated matches
Domain ID domain_idd4qc3a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4qc3b1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.2 — Bromodomain
Family Family familya.29.2.0 — automated matches
Domain ID domain_idd4qc3b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4qc3A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id4qc3B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like

8. Citations (1)

9. Files and Curves (10)