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- PDB-5fg4: Crystal structure of the bromodomain of human BRPF1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5fg4
TitleCrystal structure of the bromodomain of human BRPF1 in complex with OF-1 chemical probe
ComponentsPeregrin
KeywordsTRANSCRIPTION / Peregrin / MOZ-MORF complex
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. ...Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S.
CitationJournal: To Be Published
Title: Crystal structure of the bromodomain of human BRPF1 in complex with OF-1 chemical probe
Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S.
History
DepositionDec 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1442
Polymers13,7041
Non-polymers4401
Water1,31573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.802, 60.704, 51.171
Angle α, β, γ (deg.)90.00, 100.43, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-936-

HOH

21A-958-

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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-5XE / 4-bromanyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)-2-methyl-benzenesulfonamide


Mass: 440.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18BrN3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.92 % / Description: Rod
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 25% PEG3350, 0.1M bis-tris propane pH 7.4, 5% ethyleneglycol, 0.15M sodium nitrate
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.65→25.16 Å / Num. all: 17300 / Num. obs: 17300 / % possible obs: 99.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.028 / Net I/σ(I): 18.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.1 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.65→25.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.791 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25416 861 5 %RANDOM
Rwork0.19977 ---
obs0.20265 16439 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.602 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å22.06 Å2
2---2.2 Å20 Å2
3----1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.65→25.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 26 73 1031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02986
X-RAY DIFFRACTIONr_bond_other_d0.0010.02939
X-RAY DIFFRACTIONr_angle_refined_deg1.5892.0151336
X-RAY DIFFRACTIONr_angle_other_deg0.8193.0062154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70824.11851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43815178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.164158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2853.671455
X-RAY DIFFRACTIONr_mcbond_other3.2113.653454
X-RAY DIFFRACTIONr_mcangle_it4.7485.469568
X-RAY DIFFRACTIONr_mcangle_other4.7555.484569
X-RAY DIFFRACTIONr_scbond_it4.8094.23530
X-RAY DIFFRACTIONr_scbond_other4.8054.23531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4496.136767
X-RAY DIFFRACTIONr_long_range_B_refined9.42429.7611226
X-RAY DIFFRACTIONr_long_range_B_other9.42229.7661227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 52 -
Rwork0.298 1193 -
obs--95.92 %

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