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- PDB-6zs4: Crystal structure of the fifth bromodomain of human protein polyb... -

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Basic information

Entry
Database: PDB / ID: 6zs4
TitleCrystal structure of the fifth bromodomain of human protein polybromo-1 in complex with tert-butyl 4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazine-1-carboxylate
ComponentsProtein polybromo-1
KeywordsGENE REGULATION / BROMODOMAIN / COMPLEX / SMALL MOLECULE / STRUCTURAL GENOMICS CONSORTIUM / SGC / TRANSCRIPTION
Function / homology
Function and homology information


regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-QP8 / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPreuss, F. / Joerger, A.C. / Kraemer, A. / Wanior, M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: Pan-SMARCA/PB1 Bromodomain Inhibitors and Their Role in Regulating Adipogenesis.
Authors: Wanior, M. / Preuss, F. / Ni, X. / Kramer, A. / Mathea, S. / Gobel, T. / Heidenreich, D. / Simonyi, S. / Kahnt, A.S. / Joerger, A.C. / Knapp, S.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: 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 1.2Jan 31, 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)15,0823
Polymers14,6481
Non-polymers4342
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.270, 29.740, 36.610
Angle α, β, γ (deg.)90.000, 96.410, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 14648.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U86
#2: Chemical ChemComp-QP8 / tert-butyl 4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazine-1-carboxylate / ~{tert}-butyl 4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazine-1-carboxylate


Mass: 371.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N5O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 82 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 5000 MME, 0.2 M (NH4)2SO4, 0.1 M MES pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91842 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 2→36.4 Å / Num. obs: 9289 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 19.4431060534 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / Num. unique obs: 690 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FH7

5fh7


Resolution: 2→36.4 Å / SU ML: 0.24561713279 / Cross valid method: FREE R-VALUE / σ(F): 1.3373977252 / Phase error: 26.3296095809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230457891476 445 4.79732643381 %
Rwork0.188110312286 8831 -
obs0.190112310974 9276 98.6808510638 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.2787160071 Å2
Refinement stepCycle: LAST / Resolution: 2→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 31 82 994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071913403475938
X-RAY DIFFRACTIONf_angle_d0.7785638400371270
X-RAY DIFFRACTIONf_chiral_restr0.0420417499055139
X-RAY DIFFRACTIONf_plane_restr0.00609937575965177
X-RAY DIFFRACTIONf_dihedral_angle_d13.3243902127592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.28940.2807102335541680.2094346400012882X-RAY DIFFRACTION98.2286634461
2.2894-2.88420.2355116995311400.2119280055632924X-RAY DIFFRACTION99.2549400713
2.8842-36.38710.2087556031011370.1699769069843025X-RAY DIFFRACTION98.566084788

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