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- PDB-7jt4: Crystal Structure of BPTF bromodomain labelled with 5-fluoro-tryp... -

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Basic information

Entry
Database: PDB / ID: 7jt4
TitleCrystal Structure of BPTF bromodomain labelled with 5-fluoro-tryptophan
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION / BPTF
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 / 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
Similarity search - Domain/homology
Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsJohnson, J.A. / Shi, K. / Aihara, H. / Pomerantz, W.C.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)5T32GM008347-23 United States
CitationJournal: Org.Biomol.Chem. / Year: 2019
Title: Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor
Authors: Kirberger, S.E. / Ycas, P.D. / Johnson, J.A. / Chen, C. / Ciccone, M.F. / Woo, R.W.L. / Urick, A.K. / Zahid, H. / Shi, K. / Aihara, H. / McAllister, S.D. / Kashani-Sabet, M. / Shi, J. / ...Authors: Kirberger, S.E. / Ycas, P.D. / Johnson, J.A. / Chen, C. / Ciccone, M.F. / Woo, R.W.L. / Urick, A.K. / Zahid, H. / Shi, K. / Aihara, H. / McAllister, S.D. / Kashani-Sabet, M. / Shi, J. / Dickson, A. / Dos Santos, C.O. / Pomerantz, W.C.K.
History
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Nucleosome-remodeling factor subunit BPTF


Theoretical massNumber of molelcules
Total (without water)15,4261
Polymers15,4261
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7390 Å2
Unit cell
Length a, b, c (Å)27.335, 66.763, 39.260
Angle α, β, γ (deg.)90.000, 105.020, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 15426.413 Da / Num. of mol.: 1 / Fragment: bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12830
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) polyethylene glycol 1500 and 10% (w/v) proprionate-cacodylate-bis tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→26.4 Å / Num. obs: 7452 / % possible obs: 88.59 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19.77
Reflection shellResolution: 2.065→2.139 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 9.55 / Num. unique obs: 761 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZS

3qzs


Resolution: 2.06→19.96 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 389 5.22 %
Rwork0.1652 7057 -
obs0.1664 7446 88.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.2 Å2 / Biso mean: 17.1119 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 2.06→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 0 207 1216
Biso mean---27.43 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021047
X-RAY DIFFRACTIONf_angle_d0.5071415
X-RAY DIFFRACTIONf_dihedral_angle_d22.218403
X-RAY DIFFRACTIONf_chiral_restr0.05148
X-RAY DIFFRACTIONf_plane_restr0.005183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.360.22841040.17751920202473
2.36-2.970.20091370.1752532266995
2.97-19.960.16511480.15512605275397
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)
10.38410.2219-0.51111.8102-0.5791.0281-0.06720.07860.1334-0.16890.19920.3634-0.0128-0.3912-0.0070.1209-0.002-0.03810.0370.01030.1139-0.698120.418387.4845
21.69031.1196-0.21250.7687-0.38311.3939-0.1355-0.1431-0.72180.05060.0284-0.28660.30630.3267-0.17740.10790.07290.04160.10880.010.138613.0534-0.038691.1692
31.5998-1.032-0.43242.5152-0.47791.09050.0142-0.11280.4103-0.3004-0.0102-0.8456-0.21610.23510.03550.0958-0.0366-0.03060.0899-0.01920.072711.426216.294888.2207
41.18010.06660.12542.004-0.16461.3808-0.15730.0258-0.00150.08180.32080.2332-0.0528-0.25230.14190.0498-0.0347-0.01730.0065-0.0413-0.00530.40878.609184.7512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 90 )A57 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 108 )A91 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 129 )A109 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 178 )A130 - 178

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