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- PDB-5pgg: PanDDA analysis group deposition -- Crystal Structure of BAZ2B af... -

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Basic information

Entry
Database: PDB / ID: 5pgg
TitlePanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 180)
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsDNA BINDING PROTEIN / PanDDA / SGC - Diamond I04-1 fragment screening / bromodomain / epigenetics
Function / homology
Function and homology information


chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
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 / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.68 Å
AuthorsPearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. ...Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Renjie, Z. / Dias, A. / Vollmar, M. / Ng, J. / Brennan, P.E. / Cox, O. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: Nat Commun / Year: 2017
Title: A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Authors: Pearce, N.M. / Krojer, T. / Bradley, A.R. / Collins, P. / Nowak, R.P. / Talon, R. / Marsden, B.D. / Kelm, S. / Shi, J. / Deane, C.M. / von Delft, F.
History
DepositionFeb 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_deposit_group
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_deposit_group.group_title / _pdbx_deposit_group.group_type
Revision 1.2Oct 4, 2017Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_title
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1522
Polymers16,0901
Non-polymers621
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.905, 95.947, 57.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2168-

HOH

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Components

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


Mass: 16090.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: escherichia coli (E. coli) / References: UniProt: Q9UIF8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.18 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG600 -- 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.68→28.93 Å / Num. obs: 25194 / % possible obs: 96.2 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.039 / Rrim(I) all: 0.097 / Net I/σ(I): 9.6 / Num. measured all: 137558 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.712.30.65321399180.5150.4380.7950.967.7
9.07-28.936.10.03811971960.9980.0160.04129.197.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0131refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3G0L

3g0l


Resolution: 1.68→28.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.746 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1255 5 %RANDOM
Rwork0.19 ---
obs0.1918 23887 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 32.136 Å2 / Biso min: 17.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å2-0 Å2
2---1.46 Å20 Å2
3----1.46 Å2
Refinement stepCycle: final / Resolution: 1.68→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 4 204 1138
Biso mean--34.71 45.31 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.019968
X-RAY DIFFRACTIONr_bond_other_d0.0040.02916
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9751305
X-RAY DIFFRACTIONr_angle_other_deg1.0732126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02724.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25315181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.044155
X-RAY DIFFRACTIONr_chiral_restr0.1130.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211064
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02209
X-RAY DIFFRACTIONr_mcbond_it3.0432.84464
X-RAY DIFFRACTIONr_mcbond_other3.0472.83463
X-RAY DIFFRACTIONr_mcangle_it4.2394.227580
LS refinement shellResolution: 1.684→1.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 68 -
Rwork0.389 1319 -
all-1387 -
obs--72.85 %

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