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- PDB-7r8r: Physachenolide C with Bromodomain (BRD3-BD1) -

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Basic information

Entry
Database: PDB / ID: 7r8r
TitlePhysachenolide C with Bromodomain (BRD3-BD1)
ComponentsBromodomain-containing protein 3
KeywordsSIGNALING PROTEIN / bromodomain 3 / physachenolide C / prostate cancer
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Physachenolide C / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFromme, R. / Sivinski, J. / Zerio, C. / Gunatilaka, A.A.L. / Chapman, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Physachenolide C is a Potent, Selective BET Inhibitor.
Authors: Zerio, C.J. / Sivinski, J. / Wijeratne, E.M.K. / Xu, Y.M. / Ngo, D.T. / Ambrose, A.J. / Villa-Celis, L. / Ghadirian, N. / Clarkson, M.W. / Zhang, D.D. / Horton, N.C. / Gunatilaka, A.A.L. / ...Authors: Zerio, C.J. / Sivinski, J. / Wijeratne, E.M.K. / Xu, Y.M. / Ngo, D.T. / Ambrose, A.J. / Villa-Celis, L. / Ghadirian, N. / Clarkson, M.W. / Zhang, D.D. / Horton, N.C. / Gunatilaka, A.A.L. / Fromme, R. / Chapman, E.
History
DepositionJun 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9152
Polymers14,3691
Non-polymers5471
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.098, 49.316, 60.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Bromodomain-containing protein 3 / / RING3-like protein


Mass: 14368.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Chemical ChemComp-8L6 / Physachenolide C


Mass: 546.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 10mM CaCl, 50mM Tris-HCl pH 8.5, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→44.1 Å / Num. obs: 12117 / % possible obs: 94.55 % / Redundancy: 5.8 % / Biso Wilson estimate: 34.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.076 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 508 / CC1/2: 0.557 / % possible all: 71.21

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s91

3s91


Resolution: 1.8→44.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.7 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 554 4.6 %RANDOM
Rwork0.1584 ---
obs0.162 11563 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 128.91 Å2 / Biso mean: 43.839 Å2 / Biso min: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å2-0 Å20 Å2
2--1.24 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 1.8→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 39 58 1050
Biso mean--40.22 49.75 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131027
X-RAY DIFFRACTIONr_bond_other_d0.0010.016974
X-RAY DIFFRACTIONr_angle_refined_deg2.2851.7271405
X-RAY DIFFRACTIONr_angle_other_deg1.5581.6422248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92525.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80115183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.536152
X-RAY DIFFRACTIONr_chiral_restr0.1970.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021118
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02233
X-RAY DIFFRACTIONr_rigid_bond_restr4.67931995
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 21 -
Rwork0.203 627 -
all-648 -
obs--69.01 %

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