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- PDB-5owa: Crystal structure of the human BRPF1 bromodomain in complex with BZ054 -

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Basic information

Entry
Database: PDB / ID: 5owa
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ054
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 / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / 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 / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / 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 / 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, 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionAug 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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
B: Peregrin
C: Peregrin
D: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8607
Polymers54,8154
Non-polymers1,0453
Water6,143341
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers13,7041
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers13,7041
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers13,7041
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peregrin


Theoretical massNumber of molelcules
Total (without water)13,7041
Polymers13,7041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.889, 92.299, 81.217
Angle α, β, γ (deg.)90.00, 101.22, 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.: 4
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-B0H / ~{N}-[4-[[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]methyl]-1,3-thiazol-2-yl]-2,4-dimethyl-1,3-oxazole-5-carboxamide


Mass: 348.463 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H24N4O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 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: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.95→39.93 Å / Num. obs: 34898 / % possible obs: 94.9 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.469 / Num. unique obs: 5200 / CC1/2: 0.762 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.95→39.93 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.51
RfactorNum. reflection% reflection
Rfree0.2677 2004 5.75 %
Rwork0.2191 --
obs0.222 34857 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 72 341 4042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073807
X-RAY DIFFRACTIONf_angle_d1.0255149
X-RAY DIFFRACTIONf_dihedral_angle_d18.062364
X-RAY DIFFRACTIONf_chiral_restr0.047558
X-RAY DIFFRACTIONf_plane_restr0.006670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.39381420.3092374X-RAY DIFFRACTION97
1.9988-2.05280.37271450.28442424X-RAY DIFFRACTION96
2.0528-2.11320.33141410.27182260X-RAY DIFFRACTION94
2.1132-2.18140.3241420.2752346X-RAY DIFFRACTION94
2.1814-2.25940.34141460.262266X-RAY DIFFRACTION93
2.2594-2.34980.31461290.27042333X-RAY DIFFRACTION93
2.3498-2.45680.27811420.27422257X-RAY DIFFRACTION93
2.4568-2.58630.32111410.26652234X-RAY DIFFRACTION91
2.5863-2.74830.33591480.29162312X-RAY DIFFRACTION93
2.7483-2.96040.33491460.26082350X-RAY DIFFRACTION95
2.9604-3.25820.29121440.23042390X-RAY DIFFRACTION96
3.2582-3.72940.25761480.18582468X-RAY DIFFRACTION99
3.7294-4.69740.18561520.16152451X-RAY DIFFRACTION98
4.6974-39.94130.20191380.17452388X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -3.113 Å / Origin y: 15.2255 Å / Origin z: 56.7041 Å
111213212223313233
T0.1799 Å20.0173 Å20.008 Å2-0.1905 Å2-0.0095 Å2--0.1867 Å2
L-0.0374 °20.1201 °2-0.2562 °2-0.3872 °20.0795 °2--0.296 °2
S-0.0065 Å °0.0274 Å °0.0115 Å °0.0803 Å °0.0208 Å °0.0533 Å °0.0099 Å °0.0946 Å °-0.0158 Å °
Refinement TLS groupSelection details: all

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