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- PDB-6zn6: Protein polybromo-1 (PB1 BD2) Bound To MW278 -

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Basic information

Entry
Database: PDB / ID: 6zn6
TitleProtein polybromo-1 (PB1 BD2) Bound To MW278
ComponentsProtein polybromo-1
KeywordsPROTEIN BINDING / Bromodomain Inhibitor Epigenetics
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / 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 (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / 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 (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / 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-QMT / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPreuss, F. / Mathea, S. / Chatterjee, D. / Wanior, M. / Joerger, A.C. / Knapp, S.
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 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 1.2May 5, 2021Group: Refinement description / Category: pdbx_refine_tls_group
Revision 1.3Jan 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)27,2505
Polymers26,4632
Non-polymers7873
Water1,928107
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5942
Polymers13,2311
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6563
Polymers13,2311
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.525, 73.193, 105.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -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: 13231.299 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-QMT / 2-[6-azanyl-5-[(3~{R})-3-phenoxypiperidin-1-yl]pyridazin-3-yl]phenol / MW278


Mass: 362.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M NaCl 25% (w/v) PEG3350 0.1 M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.02→36.6 Å / Num. obs: 18158 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.9
Reflection shellResolution: 2.02→2.09 Å / Num. unique obs: 1777 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
xia2data reduction
Aimless7.0.078data scaling
PHASER7.0.078phasing
REFMAC7.0.078refinement
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HMF

3hmf


Resolution: 2.02→36.6 Å / SU ML: 0.3811 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 31.2598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.278 860 4.74 %
Rwork0.2181 17297 -
obs0.221 18157 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.54 Å2
Refinement stepCycle: LAST / Resolution: 2.02→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 58 107 1963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811895
X-RAY DIFFRACTIONf_angle_d0.86722559
X-RAY DIFFRACTIONf_chiral_restr0.0431284
X-RAY DIFFRACTIONf_plane_restr0.006361
X-RAY DIFFRACTIONf_dihedral_angle_d11.8452301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.150.43831410.34342840X-RAY DIFFRACTION100
2.15-2.310.36231370.2862840X-RAY DIFFRACTION99.87
2.31-2.540.30271330.23252869X-RAY DIFFRACTION99.83
2.54-2.910.32251330.22482866X-RAY DIFFRACTION99.97
2.91-3.670.26431730.20842871X-RAY DIFFRACTION99.9
3.67-36.60.19781430.16233011X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 12.4609437206 Å / Origin y: 13.4159787053 Å / Origin z: 13.089626006 Å
111213212223313233
T0.147597434964 Å20.0143220516697 Å20.0188364641877 Å2-0.13424011539 Å2-0.0135592015302 Å2--0.15009672976 Å2
L0.462118790467 °2-0.291806770429 °20.340521645035 °2-0.523391575145 °2-0.390728426358 °2--0.393427573526 °2
S-0.00860613450668 Å °-0.00966664611879 Å °-0.0356323393356 Å °0.00803771486518 Å °0.025552062419 Å °0.0379752103713 Å °0.0185917268245 Å °-0.0065260436374 Å °0.00619256671147 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A177 - 301
2X-RAY DIFFRACTION1B177 - 302

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