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- PDB-6znv: Protein polybromo-1 (PB1 BD2) Bound To DP28 -

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Basic information

Entry
Database: PDB / ID: 6znv
TitleProtein polybromo-1 (PB1 BD2) Bound To DP28
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
ACETATE ION / Chem-QMW / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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
Item: _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8057
Polymers13,2311
Non-polymers5746
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-45 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.706, 50.370, 33.582
Angle α, β, γ (deg.)90.000, 97.429, 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

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Protein , 1 types, 1 molecules A

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


Mass: 13231.299 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

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Non-polymers , 6 types, 144 molecules

#2: Chemical ChemComp-QMW / 1-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperidin-4-ol / DP28


Mass: 286.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.005 M zinc acetate 20% (w/v) PEG 3350

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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: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.14→41.5 Å / Num. obs: 43994 / % possible obs: 87.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.17 Å2 / CC1/2: 0.998 / Net I/σ(I): 24.7
Reflection shellResolution: 1.14→1.18 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2536 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
xia2data reduction
Aimless7.0.078data scaling
PHASER7.0.078phasing
REFMAC7.0.078refinement
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HMF

3hmf


Resolution: 1.14→41.5 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.63 / Phase error: 25.8161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2054 2163 4.92 %
Rwork0.1921 41831 -
obs0.1928 43994 87.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.04 Å2
Refinement stepCycle: LAST / Resolution: 1.14→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 32 138 1059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052935
X-RAY DIFFRACTIONf_angle_d0.82591265
X-RAY DIFFRACTIONf_chiral_restr0.0674143
X-RAY DIFFRACTIONf_plane_restr0.0072175
X-RAY DIFFRACTIONf_dihedral_angle_d7.4988144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.5721790.51021500X-RAY DIFFRACTION47.09
1.17-1.20.35261190.3751991X-RAY DIFFRACTION63
1.2-1.230.37061460.33342724X-RAY DIFFRACTION86.73
1.23-1.260.31551430.32472903X-RAY DIFFRACTION90.76
1.26-1.30.27471550.31152909X-RAY DIFFRACTION91.57
1.3-1.350.23091530.24932934X-RAY DIFFRACTION91.66
1.35-1.410.23161370.2142865X-RAY DIFFRACTION89.4
1.41-1.470.21081350.18492856X-RAY DIFFRACTION89.74
1.47-1.550.1831620.16792995X-RAY DIFFRACTION93.99
1.55-1.640.19441700.17053014X-RAY DIFFRACTION94.68
1.64-1.770.20141440.16873021X-RAY DIFFRACTION94.14
1.77-1.950.21441380.18042881X-RAY DIFFRACTION88.87
1.95-2.230.16831650.17193078X-RAY DIFFRACTION96.55
2.23-2.810.17561880.18143096X-RAY DIFFRACTION96.67
2.81-41.50.21211290.18023064X-RAY DIFFRACTION92.77
Refinement TLS params.Method: refined / Origin x: 27.8381741944 Å / Origin y: 6.87328793108 Å / Origin z: 11.2150900936 Å
111213212223313233
T0.106848659955 Å2-0.00429797080739 Å2-0.0161338235478 Å2-0.107437422076 Å2-0.00151637116675 Å2--0.0724953919528 Å2
L2.27849822697 °20.692440628983 °2-0.613013140542 °2-0.521377711939 °2-0.0233261716598 °2--0.680848622629 °2
S-0.0407227899368 Å °0.000871111952608 Å °-0.187648718528 Å °-0.00937176076158 Å °-0.028803684083 Å °-0.0115643057796 Å °0.0769669238771 Å °-0.0408053256926 Å °0.0602804961943 Å °
Refinement TLS groupSelection details: all

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