6fi1

Crystal structure of human BAZ2B PHD zinc finger in complex with Fr23

Method: X-RAY DIFFRACTION Dmax: 68.6 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1928–1983 Not recorded ZN ZINC ION × 2 D3H ~{N}-(4-aminophenyl)-2-azanyl-ethanamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;291 K;2.2-2.4 M sodium/potassium phopsphate Resolution 2.70 Å R-free 0.300
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1928–1983 Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;291 K;2.2-2.4 M sodium/potassium phopsphate Resolution 2.70 Å R-free 0.300

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 3–58; UniProt 1928–1983 Author chain B; PDBConstruct 3–58; UniProt 1928–1983

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 6fi1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6fi1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6fi1
Deposition date deposition_date2018-01-16
Structure title titleCrystal structure of human BAZ2B PHD zinc finger in complex with Fr23
Keywords keywordsTRANSCRIPTION, PHD, zinc finger, BAZ2B, BAZ2A, bromodomain, fragment, epigenetic; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.66
Radius of gyration Rg (electron density) rg_electron14.95
Forward intensity I(0) i03793370.00
Molecular weight molecular_weight12850.0 kDa
Excluded volume excluded_volume15634 ų
Envelope volume envelope_volume19038 ų
Hydration-shell volume shell_volume11362 ų
Envelope diameter envelope_diameter66.7
Shell Rg shell_rg20.16
Envelope Rg envelope_rg15.81
Shape Rg shape_rg14.93
Total Rg total_rg16.04
Total atoms total_atoms872
Residues n_residues113
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 dmax68.6
Rg (real space) rg_real15.72
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real3.7930e+06
I(0) uncertainty (real space) i0_real_error5.2990e+04
Rg (reciprocal space) rg_reciprocal15.71
I(0) (reciprocal space) i0_reciprocal3793000.0000
Solution quality estimate total_estimate0.6186
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.2
Skewness Skewness skewness0.554
Kurtosis Kurtosis kurtosis0.467
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha474900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.241; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.314; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6fi1a1
Class classg — Small proteins
Fold Fold foldg.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamilyg.50.1 — FYVE/PHD zinc finger
Family Family familyg.50.1.0 — automated matches
Domain ID domain_idd6fi1a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6fi1b1
Class classg — Small proteins
Fold Fold foldg.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamilyg.50.1 — FYVE/PHD zinc finger
Family Family familyg.50.1.0 — automated matches
Domain ID domain_idd6fi1b2
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_id6fi1A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id6fi1B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)

8. Citations (1)

9. Files and Curves (10)