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- PDB-5o5f: Crystal structure of the human BRPF1 bromodomain in complex with BZ038 -

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Basic information

Entry
Database: PDB / ID: 5o5f
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ038
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9LT / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.302 Å
AuthorsZhu, J. / Caflisch, A.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Structure-based discovery of selective BRPF1 bromodomain inhibitors.
Authors: Zhu, J. / Zhou, C. / Caflisch, A.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2494
Polymers13,7041
Non-polymers5453
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint2 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.765, 60.765, 63.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1016-

HOH

21A-1064-

HOH

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-9LT / 1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide


Mass: 421.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20FN5O3
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane, pH6.5, 0.2 M Sodium Nitrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→40.52 Å / Num. obs: 33637 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.022 / Net I/σ(I): 37.3
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1591 / CC1/2: 0.802 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementStarting model: 4LC2

4lc2


Resolution: 1.302→30.382 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.64
RfactorNum. reflection% reflection
Rfree0.1878 2005 5.97 %
Rwork0.1752 --
obs0.176 33607 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.302→30.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 39 223 1198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081042
X-RAY DIFFRACTIONf_angle_d0.7791415
X-RAY DIFFRACTIONf_dihedral_angle_d5.028644
X-RAY DIFFRACTIONf_chiral_restr0.07147
X-RAY DIFFRACTIONf_plane_restr0.005189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3018-1.33440.26371370.23522183X-RAY DIFFRACTION97
1.3344-1.37050.23261410.21452231X-RAY DIFFRACTION100
1.3705-1.41080.20591390.20842244X-RAY DIFFRACTION100
1.4108-1.45630.22851390.1982216X-RAY DIFFRACTION100
1.4563-1.50840.18881440.18112225X-RAY DIFFRACTION100
1.5084-1.56880.20521450.17442265X-RAY DIFFRACTION100
1.5688-1.64020.19171450.17042253X-RAY DIFFRACTION100
1.6402-1.72660.17991400.17322226X-RAY DIFFRACTION100
1.7266-1.83480.18681450.18072262X-RAY DIFFRACTION100
1.8348-1.97640.18921450.17942239X-RAY DIFFRACTION100
1.9764-2.17530.19311440.1672274X-RAY DIFFRACTION100
2.1753-2.48990.17941420.16982276X-RAY DIFFRACTION100
2.4899-3.13650.18181480.18222309X-RAY DIFFRACTION100
3.1365-30.39080.18131510.16542399X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.6128 Å / Origin y: 1.7403 Å / Origin z: -9.6875 Å
111213212223313233
T0.1749 Å20.0269 Å20.0012 Å2-0.0983 Å20.0001 Å2--0.1172 Å2
L1.6502 °2-0.2632 °20.7321 °2-0.7863 °20.2674 °2--0.9794 °2
S-0.0798 Å °-0.1473 Å °-0.0556 Å °0.113 Å °0.0437 Å °0.0225 Å °0.0474 Å °-0.0503 Å °-0.0031 Å °
Refinement TLS groupSelection details: all

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