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- PDB-5hrv: Crystal structure of the fifth bromodomain of human PB1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5hrv
TitleCrystal structure of the fifth bromodomain of human PB1 in complex with 1-ethylisochromeno[3,4-c]pyrazol-5(2H)-one) compound
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / BRM1 / BRG1-associated factor 180 / chromatin remodeling
Function / homology
Function and homology information


regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group ...Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1-ethylisochromeno[3,4-c]pyrazol-5(3H)-one / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTallant, C. / Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Newman, J.A. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Mikros, E. / Knapp, S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis.
Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / ...Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / Savitsky, P. / Bagratuni, T. / Kastritis, E. / Terpos, E. / Filippakopoulos, P. / Muller, S. / Skaltsounis, A.L. / Downs, J.A. / Knapp, S. / Mikros, E.
History
DepositionJan 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9243
Polymers14,6481
Non-polymers2762
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.817, 140.272, 41.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein polybromo-1 / hPB1 / BRG1-associated factor 180 / BAF180 / Polybromo-1D / PB1 fifth bromodomain


Mass: 14648.000 Da / Num. of mol.: 1 / Fragment: UNP Residues 613-734
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U86
#2: Chemical ChemComp-64C / 1-ethylisochromeno[3,4-c]pyrazol-5(3H)-one


Mass: 214.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.88 Å3/Da / Density % sol: 57.32 % / Description: Plate crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M tris-sodium citrate dihydrate pH 5.6, 20% isopropanol, 20% PEG4K
PH range: 5.6-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 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: 1.7→28.91 Å / Num. all: 19011 / Num. obs: 19011 / % possible obs: 99.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.043 / Rsym value: 0.023 / Net I/σ(I): 28.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.9 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G0J

3g0j


Resolution: 1.7→28.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.77 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 941 5 %RANDOM
Rwork0.1778 ---
obs0.1793 18059 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.867 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---1.45 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.7→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 20 99 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021010
X-RAY DIFFRACTIONr_bond_other_d0.0030.02977
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.0131358
X-RAY DIFFRACTIONr_angle_other_deg1.0083.0032255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0875118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80923.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17515202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.942159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
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_it1.8582.323463
X-RAY DIFFRACTIONr_mcbond_other1.8592.316462
X-RAY DIFFRACTIONr_mcangle_it2.7473.462578
X-RAY DIFFRACTIONr_mcangle_other2.7453.471579
X-RAY DIFFRACTIONr_scbond_it3.282.764547
X-RAY DIFFRACTIONr_scbond_other3.2782.762548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2613.94779
X-RAY DIFFRACTIONr_long_range_B_refined7.03619.3111284
X-RAY DIFFRACTIONr_long_range_B_other7.03319.3111285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 54 -
Rwork0.258 1213 -
obs--91.02 %

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