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- PDB-5mwg: Crystal structure of the human BRPF1 bromodomain in complex with BZ091 -

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Basic information

Entry
Database: PDB / ID: 5mwg
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ091
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-WGX / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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 / 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 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Peregrin
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4355
Polymers27,4072
Non-polymers1,0273
Water8,053447
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2483
Polymers13,7041
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1862
Polymers13,7041
Non-polymers4831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.586, 61.089, 48.590
Angle α, β, γ (deg.)90.00, 101.63, 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-WGX / ~{N}-[1,4-dimethyl-2,3-bis(oxidanylidene)-7-piperidin-1-yl-quinoxalin-6-yl]-5,6,7,8-tetrahydronaphthalene-2-sulfonamide


Mass: 482.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30N4O4S
#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.: 447 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
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: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 1.5→47.59 Å / Num. obs: 40168 / % possible obs: 90.2 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.5→47.59 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 22.69
RfactorNum. reflection% reflection
Rfree0.2272 1995 4.97 %
Rwork0.2014 --
obs0.2026 40142 89.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 72 447 2342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061986
X-RAY DIFFRACTIONf_angle_d0.8642695
X-RAY DIFFRACTIONf_dihedral_angle_d12.8551690
X-RAY DIFFRACTIONf_chiral_restr0.048281
X-RAY DIFFRACTIONf_plane_restr0.007348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.23461500.22232803X-RAY DIFFRACTION93
1.5375-1.57910.29971460.21232789X-RAY DIFFRACTION93
1.5791-1.62560.23361540.22122810X-RAY DIFFRACTION93
1.6256-1.67810.2621460.21162792X-RAY DIFFRACTION93
1.6781-1.7380.23331500.20092823X-RAY DIFFRACTION92
1.738-1.80760.27481410.21162642X-RAY DIFFRACTION89
1.8076-1.88990.27341440.21572602X-RAY DIFFRACTION87
1.8899-1.98950.29971430.21622748X-RAY DIFFRACTION91
1.9895-2.11420.21131400.19932732X-RAY DIFFRACTION89
2.1142-2.27740.20691310.19352640X-RAY DIFFRACTION88
2.2774-2.50660.22141290.20582657X-RAY DIFFRACTION88
2.5066-2.86930.23361310.21322628X-RAY DIFFRACTION85
2.8693-3.61480.22161470.18922753X-RAY DIFFRACTION91
3.6148-47.61670.20361430.19472728X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 1.7397 Å / Origin y: -5.8312 Å / Origin z: 8.8255 Å
111213212223313233
T0.1387 Å2-0.0068 Å2-0.0105 Å2-0.1513 Å20.0008 Å2--0.1428 Å2
L0.4655 °2-0.0513 °2-0.2142 °2-0.683 °20.0087 °2--0.6074 °2
S0.0126 Å °-0.044 Å °-0.0137 Å °0.0492 Å °0.0102 Å °-0.0252 Å °0.0296 Å °0.0032 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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