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- PDB-5owb: Crystal structure of the human BRPF1 bromodomain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5owb
TitleCrystal structure of the human BRPF1 bromodomain in complex with DSPBP1004
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
4-methyl-6-oxidanyl-1-benzofuran-3-one / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZhu, J. / Spiliotopoulos, D. / Caflisch, A.
CitationJournal: To Be Published
Title: Crystal structure of the human BRPF1 bromodomain in complex with DSPBP1004
Authors: Zhu, J. / Caflisch, A.
History
DepositionAug 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9303
Polymers13,7041
Non-polymers2262
Water3,009167
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint2 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.426, 60.426, 63.468
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-991-

HOH

21A-1029-

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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-AYW / 4-methyl-6-oxidanyl-1-benzofuran-3-one


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Acetate, pH5.5, 0.15 M Sodium Nitrate, 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: 1.65→40.38 Å / Num. obs: 16528 / % possible obs: 99.8 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.7
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 815 / CC1/2: 0.924

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Processing

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

4lc2


Resolution: 1.65→40.376 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.2044 1650 9.99 %
Rwork0.1746 --
obs0.1776 16509 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→40.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 16 167 1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007990
X-RAY DIFFRACTIONf_angle_d0.8311340
X-RAY DIFFRACTIONf_dihedral_angle_d9.19845
X-RAY DIFFRACTIONf_chiral_restr0.046142
X-RAY DIFFRACTIONf_plane_restr0.004178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6503-1.69890.26431380.24071217X-RAY DIFFRACTION99
1.6989-1.75370.2591380.22591227X-RAY DIFFRACTION100
1.7537-1.81640.24921320.19251207X-RAY DIFFRACTION99
1.8164-1.88910.21651400.18591229X-RAY DIFFRACTION100
1.8891-1.97510.23561340.19611225X-RAY DIFFRACTION100
1.9751-2.07920.21641350.18541219X-RAY DIFFRACTION100
2.0792-2.20950.20511360.17131220X-RAY DIFFRACTION100
2.2095-2.38010.19141410.17561234X-RAY DIFFRACTION99
2.3801-2.61950.20491340.17881238X-RAY DIFFRACTION100
2.6195-2.99850.22661400.18031253X-RAY DIFFRACTION100
2.9985-3.77740.16581380.1581273X-RAY DIFFRACTION100
3.7774-40.38790.20321440.16371317X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.927 Å / Origin y: 22.8204 Å / Origin z: 0.3936 Å
111213212223313233
T0.1828 Å2-0.0632 Å20.0208 Å2-0.147 Å2-0.0111 Å2--0.1128 Å2
L1.8142 °2-0.0077 °2-0.7456 °2-2.8446 °21.2965 °2--1.976 °2
S0.0254 Å °-0.2024 Å °0.0887 Å °0.4351 Å °-0.1264 Å °-0.0891 Å °0.0983 Å °0.0821 Å °-0.0623 Å °
Refinement TLS groupSelection details: all

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