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- PDB-5o5h: Crystal structure of the human BRPF1 bromodomain in complex with BZ053 -

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Basic information

Entry
Database: PDB / ID: 5o5h
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ053
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-9LK / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4534
Polymers13,7041
Non-polymers7503
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area7130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.027, 61.027, 63.787
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-975-

HOH

21A-1002-

HOH

31A-1016-

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-9LK / ~{N}-[6-(4-chloranylphenoxy)pyridin-3-yl]-2,4-dimethyl-1,3-oxazole-5-carboxamide


Mass: 343.764 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14ClN3O3
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
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 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40.7 Å / Num. obs: 12134 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.014 / Net I/σ(I): 43.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 5.4 / Num. measured obs: 14203 / Num. unique obs: 740 / CC1/2: 0.955 / Rpim(I) all: 0.212 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.85→40.697 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2346 1171 9.94 %
Rwork0.1901 --
obs0.1944 11778 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→40.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 52 122 1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081030
X-RAY DIFFRACTIONf_angle_d1.0981394
X-RAY DIFFRACTIONf_dihedral_angle_d11.893865
X-RAY DIFFRACTIONf_chiral_restr0.049142
X-RAY DIFFRACTIONf_plane_restr0.004184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.93430.461250.4091118X-RAY DIFFRACTION84
1.9343-2.03630.27871440.25551311X-RAY DIFFRACTION97
2.0363-2.16380.26261510.21331336X-RAY DIFFRACTION100
2.1638-2.33090.27831370.22021300X-RAY DIFFRACTION97
2.3309-2.56540.24681530.18541345X-RAY DIFFRACTION100
2.5654-2.93650.23341520.1971372X-RAY DIFFRACTION100
2.9365-3.69940.20181460.18011370X-RAY DIFFRACTION100
3.6994-40.70650.21331630.15881455X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.0163 Å / Origin y: -22.6332 Å / Origin z: 0.9119 Å
111213212223313233
T0.3052 Å2-0.1229 Å2-0.0427 Å2-0.2681 Å20.0347 Å2--0.2259 Å2
L2.3556 °2-0.5268 °20.7729 °2-2.9476 °2-0.8369 °2--2.185 °2
S-0.0119 Å °-0.261 Å °-0.1108 Å °0.5138 Å °-0.1025 Å °-0.0011 Å °-0.0991 Å °-0.1234 Å °-0.0226 Å °
Refinement TLS groupSelection details: all

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