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- PDB-5r4g: PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROM... -

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Entry
Database: PDB / ID: 5r4g
TitlePanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000621a
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsTRANSCRIPTION / PanDDA / SGC - Diamond I04-1 fragment screening / XChemExplorer / BROMODOMAIN / BPTF / FALZ / FAC1 / BROMODOMAIN AND PHD FINGER-CONTAINING TRANSCRIPTION FACTOR / FETAL ALZ-50 CLONE 1 PROTEIN
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / 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 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Nucleosome-remodeling factor subunit BPTF / 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 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / 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
4-(1,2,3-thiadiazol-4-yl)phenyl ethylcarbamate / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.25 Å
AuthorsTalon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. ...Talon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. / MacLean, E. / Renjie, Z. / Dias, A. / Brennan, P.E. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Talon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. / MacLean, E. / Renjie, Z. / Dias, A. / Brennan, ...Authors: Talon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. / MacLean, E. / Renjie, Z. / Dias, A. / Brennan, P.E. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
History
DepositionFeb 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7833
Polymers14,4551
Non-polymers3272
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.416, 27.464, 38.423
Angle α, β, γ (deg.)90.000, 96.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleosome-remodeling factor subunit BPTF / Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal ...Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal Alzheimer antigen


Mass: 14455.415 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q12830
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-RU4 / 4-(1,2,3-thiadiazol-4-yl)phenyl ethylcarbamate


Mass: 249.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.67 % / Mosaicity: 0.43 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.25→55.86 Å / Num. obs: 30191 / % possible obs: 92 % / Redundancy: 3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.022 / Rpim(I) all: 0.015 / Rrim(I) all: 0.027 / Net I/σ(I): 19.6 / Num. measured all: 90554 / Scaling rejects: 0
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
1.25-1.322.40.291945740230.890.230.3742.284.2
3.95-55.863.10.014325110550.9990.0090.01760.695.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UV2

3uv2


Resolution: 1.25→55.88 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.944 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1467 4.9 %RANDOM
Rwork0.1839 ---
obs0.1851 28724 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.99 Å2 / Biso mean: 20.342 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.69 Å2
2---0.25 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 1.25→55.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 21 156 1160
Biso mean--38.75 30.91 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191581
X-RAY DIFFRACTIONr_bond_other_d0.0010.021220
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.991879
X-RAY DIFFRACTIONr_angle_other_deg0.962.9772852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.785178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00223.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6011510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211642
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02296
X-RAY DIFFRACTIONr_mcbond_it1.0821.749735
X-RAY DIFFRACTIONr_mcbond_other1.0871.68725
X-RAY DIFFRACTIONr_mcangle_it1.8972.523838
LS refinement shellResolution: 1.248→1.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 90 -
Rwork0.277 1935 -
all-2025 -
obs--84.62 %

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