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- PDB-6fi1: Crystal structure of human BAZ2B PHD zinc finger in complex with Fr23 -

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Basic information

Entry
Database: PDB / ID: 6fi1
TitleCrystal structure of human BAZ2B PHD zinc finger in complex with Fr23
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / PHD / zinc finger / BAZ2B / BAZ2A / bromodomain / fragment / epigenetic
Function / homology
Function and homology information


chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / DNA binding / zinc ion binding / nucleus
Similarity search - Function
BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain ...BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
~{N}-(4-aminophenyl)-2-azanyl-ethanamide / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAmato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach.
Authors: Amato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A.
History
DepositionJan 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2B
B: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5147
Polymers13,0872
Non-polymers4275
Water00
1
A: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8404
Polymers6,5441
Non-polymers2963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6753
Polymers6,5441
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.779, 45.470, 64.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2B / hWALp4


Mass: 6543.708 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-D3H / ~{N}-(4-aminophenyl)-2-azanyl-ethanamide


Mass: 165.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N3O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2-2.4 M sodium/potassium phopsphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.7→64.83 Å / Num. obs: 3349 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.219 / Net I/σ(I): 5.3
Reflection shellResolution: 2.7→2.83 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QF3

4qf3


Resolution: 2.7→37.25 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.847 / SU B: 31.856 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29994 153 4.6 %RANDOM
Rwork0.22579 ---
obs0.22951 3169 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å20 Å2-0 Å2
2--2.03 Å2-0 Å2
3---1.98 Å2
Refinement stepCycle: 1 / Resolution: 2.7→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 16 0 872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019913
X-RAY DIFFRACTIONr_bond_other_d0.0020.02826
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9891229
X-RAY DIFFRACTIONr_angle_other_deg1.1463.021911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.31624.24233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3815152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.865153
X-RAY DIFFRACTIONr_chiral_restr0.0890.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021980
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02173
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0224.811452
X-RAY DIFFRACTIONr_mcbond_other2.0174.81451
X-RAY DIFFRACTIONr_mcangle_it3.297.202562
X-RAY DIFFRACTIONr_mcangle_other3.2887.205563
X-RAY DIFFRACTIONr_scbond_it2.7284.962461
X-RAY DIFFRACTIONr_scbond_other2.7254.966462
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6247.379667
X-RAY DIFFRACTIONr_long_range_B_refined5.3255.952995
X-RAY DIFFRACTIONr_long_range_B_other5.31955.941995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 4 -
Rwork0.256 216 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.7951-1.3709-4.45637.29270.29054.12660.20280.54260.20780.11890.10770.0483-0.0252-0.6802-0.31050.0815-0.01560.00360.13040.05680.030325.61996.145511.2287
28.6057-1.03410.82722.9079-0.62217.3128-0.0830.4356-0.9310.120.18390.0840.4308-0.0139-0.10080.13120.02750.01340.0796-0.04110.102941.0579-3.20224.5319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1927 - 1983
2X-RAY DIFFRACTION2B1927 - 1982

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