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- PDB-5h6y: The BPTF Bromodomain Recognising H4K12Cr peptide -

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Basic information

Entry
Database: PDB / ID: 5h6y
TitleThe BPTF Bromodomain Recognising H4K12Cr peptide
Components
  • GLY-KCR-GLY
  • Nucleosome-remodeling factor subunit BPTF
KeywordsTRANSCRIPTION / Bromodomain / Crotonylation / Transcriptional Factor
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
Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWang, Y. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
University Grants CommitteeHK-RGC C7037-14G Hong Kong
CitationJournal: To Be Published
Title: The BPTF Bromodomain Recognising H4K12Cr peptide
Authors: Wang, Y. / Hao, Q.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleosome-remodeling factor subunit BPTF
B: GLY-KCR-GLY


Theoretical massNumber of molelcules
Total (without water)14,0382
Polymers14,0382
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.350, 71.186, 27.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 13709.612 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2921-3036
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q12830
#2: Protein/peptide GLY-KCR-GLY


Mass: 328.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 9284 / % possible obs: 99.4 % / Redundancy: 6.5 % / Net I/σ(I): 13.93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2→24.268 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.98
RfactorNum. reflection% reflection
Rfree0.2237 433 5.31 %
Rwork0.1866 --
obs0.1885 8157 88.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→24.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 0 89 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071012
X-RAY DIFFRACTIONf_angle_d0.9841366
X-RAY DIFFRACTIONf_dihedral_angle_d14.257388
X-RAY DIFFRACTIONf_chiral_restr0.038143
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.28930.28091170.20061977X-RAY DIFFRACTION69
2.2893-2.88360.27851480.21192730X-RAY DIFFRACTION95
2.8836-24.26990.19061680.17363017X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.8921 Å / Origin y: 12.5059 Å / Origin z: -7.9715 Å
111213212223313233
T1.2115 Å20.0408 Å2-0.2201 Å2-0.7417 Å2-0.3464 Å2--0.6558 Å2
L0.6007 °20.31 °20.3412 °2-0.8342 °2-1.1725 °2--2.8914 °2
S-0.1633 Å °0.1816 Å °-0.0807 Å °-0.188 Å °0.2607 Å °-0.1945 Å °0.1082 Å °0.2505 Å °-0.4185 Å °
Refinement TLS groupSelection details: chain B

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