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- PDB-6zs3: Crystal structure of the fifth bromodomain of human protein polyb... -

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Entry
Database: PDB / ID: 6zs3
TitleCrystal structure of the fifth bromodomain of human protein polybromo-1 in complex with 2-(6-amino-5-(piperazin-1-yl)pyridazin-3-yl)phenol
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 / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / 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 / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / 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 / chromatin / regulation of transcription by RNA polymerase II / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-FX5 / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPreuss, F. / Joerger, A.C. / Wanior, M. / Kraemer, A. / 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
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9656
Polymers29,2962
Non-polymers6694
Water4,017223
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0444
Polymers14,6481
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9202
Polymers14,6481
Non-polymers2721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.180, 41.190, 133.907
Angle α, β, γ (deg.)90.000, 96.347, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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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.: 2
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-FX5 / 2-(6-azanyl-5-piperazin-4-ium-1-yl-pyridazin-3-yl)phenol


Mass: 272.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% (w/v) PEG 3350, 0.2 M sodium malonate, 10% (v/v) ethylene glycol, 0.1 M bis-tris propane pH 7.1

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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: 1.67→53.6 Å / Num. obs: 35732 / % possible obs: 99.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.8127542003 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.1
Reflection shellResolution: 1.67→1.69 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1761 / CC1/2: 0.927

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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: 1.67→53.6 Å / SU ML: 0.17365359813 / Cross valid method: FREE R-VALUE / σ(F): 1.33792998612 / Phase error: 25.702421203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24307764832 1809 5.06524052192 %
Rwork0.21138609085 33905 -
obs0.213029633087 35714 99.2248492762 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.0309388265 Å2
Refinement stepCycle: LAST / Resolution: 1.67→53.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 48 223 2086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006095933334221921
X-RAY DIFFRACTIONf_angle_d0.8046980251562589
X-RAY DIFFRACTIONf_chiral_restr0.046129683747276
X-RAY DIFFRACTIONf_plane_restr0.00494214363536359
X-RAY DIFFRACTIONf_dihedral_angle_d13.97556975731223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.71010.3005562327171390.2334734282632577X-RAY DIFFRACTION99.4143484627
1.7101-1.76040.2476438489951260.2294574920952599X-RAY DIFFRACTION99.3437841779
1.7604-1.81720.2476783822151270.2210685656482609X-RAY DIFFRACTION98.8082340195
1.8172-1.88220.2663250255431310.2265945113272590X-RAY DIFFRACTION99.451754386
1.8822-1.95750.2678876116751470.2212490340052594X-RAY DIFFRACTION99.0961677513
1.9575-2.04660.2502913619011510.2214315476562572X-RAY DIFFRACTION99.343305363
2.0466-2.15450.2683090948471440.2100113927032590X-RAY DIFFRACTION99.4181818182
2.1545-2.28950.2393655233481550.2035382258872565X-RAY DIFFRACTION98.8372093023
2.2895-2.46630.2458376890911250.218916891432559X-RAY DIFFRACTION97.4582425563
2.4663-2.71450.2590426030621520.2189599715982603X-RAY DIFFRACTION98.8872936109
2.7145-3.10720.231079212071350.2243798814022643X-RAY DIFFRACTION100
3.1072-3.91460.2321992925751280.2002811238912669X-RAY DIFFRACTION99.9642601858
3.9146-53.60.2234678375931490.1957224391262735X-RAY DIFFRACTION99.9306999307

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