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- PDB-5t4u: Crystal structure of the bromodomain of human BRPF1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5t4u
TitleCrystal structure of the bromodomain of human BRPF1 in complex with a quinolinone ligand
ComponentsPeregrin
KeywordsTRANSCRIPTION / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC
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
1-METHYLQUINOLIN-2(1H)-ONE / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTallant, C. / Igoe, N. / Bayle, E.D. / Nunez-Alonso, G. / Newman, J.A. / Mathea, S. / Savitsky, P. / Fedorov, O. / Brennan, P.E. / Muller, S. ...Tallant, C. / Igoe, N. / Bayle, E.D. / Nunez-Alonso, G. / Newman, J.A. / Mathea, S. / Savitsky, P. / Fedorov, O. / Brennan, P.E. / Muller, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fish, P. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design of a Biased Potent Small Molecule Inhibitor of the Bromodomain and PHD Finger-Containing (BRPF) Proteins Suitable for Cellular and in Vivo Studies.
Authors: Igoe, N. / Bayle, E.D. / Fedorov, O. / Tallant, C. / Savitsky, P. / Rogers, C. / Owen, D.R. / Deb, G. / Somervaille, T.C. / Andrews, D.M. / Jones, N. / Cheasty, A. / Ryder, H. / Brennan, P.E. ...Authors: Igoe, N. / Bayle, E.D. / Fedorov, O. / Tallant, C. / Savitsky, P. / Rogers, C. / Owen, D.R. / Deb, G. / Somervaille, T.C. / Andrews, D.M. / Jones, N. / Cheasty, A. / Ryder, H. / Brennan, P.E. / Muller, S. / Knapp, S. / Fish, P.V.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: 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)13,9253
Polymers13,7041
Non-polymers2212
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-4 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.315, 60.315, 63.389
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-976-

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-12Q / 1-METHYLQUINOLIN-2(1H)-ONE / 1-METHYL-2-QUINOLONE


Mass: 159.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20 % PEG3350, 0.2 M ammonium nitrate / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.5→27.23 Å / Num. all: 21838 / Num. obs: 206811 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.293 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rsym value: 0.024 / Net I/σ(I): 17.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.9 / CC1/2: 0.939 / % possible all: 100

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Processing

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

4lc2


Resolution: 1.5→27.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.565 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23079 1061 4.9 %RANDOM
Rwork0.20634 ---
obs0.20755 20751 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.609 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å2-0 Å2
2---0.25 Å20 Å2
3---0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.5→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 16 116 1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019968
X-RAY DIFFRACTIONr_bond_other_d0.0010.02932
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9951302
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0022138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6915111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56724.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15715180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.165158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02234
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_it1.6542.063447
X-RAY DIFFRACTIONr_mcbond_other1.5962.057446
X-RAY DIFFRACTIONr_mcangle_it2.2973.086557
X-RAY DIFFRACTIONr_mcangle_other2.33.092558
X-RAY DIFFRACTIONr_scbond_it2.7382.429521
X-RAY DIFFRACTIONr_scbond_other2.7352.43522
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2183.523746
X-RAY DIFFRACTIONr_long_range_B_refined5.53117.9321262
X-RAY DIFFRACTIONr_long_range_B_other5.42317.5091215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 69 -
Rwork0.265 1530 -
obs--100 %

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