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- PDB-5mwh: Crystal structure of the human BRPF1 bromodomain in complex with BZ089 -

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Basic information

Entry
Database: PDB / ID: 5mwh
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ089
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 / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
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 C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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
NITRATE ION / Chem-UWX / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 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
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
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 / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 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: Peregrin
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5056
Polymers27,4072
Non-polymers1,0974
Water4,324240
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1902
Polymers13,7041
Non-polymers4871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3144
Polymers13,7041
Non-polymers6113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.689, 63.279, 49.000
Angle α, β, γ (deg.)90.00, 102.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13703.698 Da / Num. of mol.: 2
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-UWX / ~{N}-[1,4-dimethyl-7-morpholin-4-yl-2,3-bis(oxidanylidene)quinoxalin-6-yl]-4-(2-methylpropyl)benzenesulfonamide


Mass: 486.584 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30N4O5S
#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.: 240 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
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: X06SA / Wavelength: 1.000019 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000019 Å / Relative weight: 1
ReflectionResolution: 1.65→38.19 Å / Num. obs: 32567 / % possible obs: 93 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.65→38.19 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.11
RfactorNum. reflection% reflection
Rfree0.2256 1996 6.14 %
Rwork0.1789 --
obs0.1817 32525 92.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 76 240 2143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061986
X-RAY DIFFRACTIONf_angle_d0.7192692
X-RAY DIFFRACTIONf_dihedral_angle_d19.5171230
X-RAY DIFFRACTIONf_chiral_restr0.042284
X-RAY DIFFRACTIONf_plane_restr0.006348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.28651430.27312209X-RAY DIFFRACTION93
1.6913-1.7370.29711430.23982202X-RAY DIFFRACTION94
1.737-1.78810.27441500.22212178X-RAY DIFFRACTION94
1.7881-1.84580.27161440.20722196X-RAY DIFFRACTION94
1.8458-1.91180.231460.20072202X-RAY DIFFRACTION93
1.9118-1.98830.21651450.20312160X-RAY DIFFRACTION93
1.9883-2.07880.26061410.18342150X-RAY DIFFRACTION92
2.0788-2.18840.21300.17372087X-RAY DIFFRACTION88
2.1884-2.32550.19411300.17111986X-RAY DIFFRACTION85
2.3255-2.5050.25091470.18762264X-RAY DIFFRACTION96
2.505-2.7570.23411470.19292270X-RAY DIFFRACTION96
2.757-3.15580.20771450.18482239X-RAY DIFFRACTION95
3.1558-3.97530.20971360.15852150X-RAY DIFFRACTION91
3.9753-38.20350.22891490.16962236X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 1.7314 Å / Origin y: 4.4891 Å / Origin z: 8.4958 Å
111213212223313233
T0.2536 Å2-0.0114 Å2-0.0043 Å2-0.2392 Å20.0003 Å2--0.2438 Å2
L0.9303 °2-0.2041 °20.0548 °2-0.9351 °2-0.022 °2--0.724 °2
S-0.0524 Å °-0.0028 Å °-0.0101 Å °0.0416 Å °0.0655 Å °-0.0226 Å °0.0528 Å °-0.0779 Å °0 Å °
Refinement TLS groupSelection details: all

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