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- PDB-5r4o: PanDDA analysis group deposition of ground-state model of BROMODO... -

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Basic information

Entry
Database: PDB / ID: 5r4o
TitlePanDDA analysis group deposition of ground-state model of BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF
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 / chromatin / regulation of DNA-templated transcription / 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 / metal ion binding / nucleus / 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
Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.05 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 of ground-state model
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 25, 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)14,7344
Polymers14,4551
Non-polymers2783
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.800, 27.370, 38.320
Angle α, β, γ (deg.)90.000, 96.200, 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 / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.02 Å3/Da / Density % sol: 38.99 % / Mosaicity: 0 °
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 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.05→55.57 Å / Num. obs: 40315 / % possible obs: 75.6 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Net I/σ(I): 15.8 / Num. measured all: 107275 / 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
1.05-1.0810.6723703530.5970.6720.951.29.2
4.72-55.5730.03219176370.9980.0220.0435.497.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UV2

3uv2


Resolution: 1.05→55.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.485 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 1966 4.9 %RANDOM
Rwork0.1687 ---
obs0.1691 38348 75.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.21 Å2 / Biso mean: 14.473 Å2 / Biso min: 5.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.37 Å2
2---0.37 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.05→55.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 16 154 1153
Biso mean--21.66 24.62 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.021083
X-RAY DIFFRACTIONr_bond_other_d0.0030.02995
X-RAY DIFFRACTIONr_angle_refined_deg2.6121.9851478
X-RAY DIFFRACTIONr_angle_other_deg1.21632325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3685136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02724.03557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18115193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.831158
X-RAY DIFFRACTIONr_chiral_restr0.1660.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_mcbond_it2.0941.249496
X-RAY DIFFRACTIONr_mcbond_other2.0361.235494
X-RAY DIFFRACTIONr_mcangle_it3.2871.858622
LS refinement shellResolution: 1.055→1.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 13 -
Rwork0.315 343 -
all-356 -
obs--9.13 %

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