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- PDB-8fta: Crystal Structure of the second bromodomain of human Polybromo-1 ... -

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Basic information

Entry
Database: PDB / ID: 8fta
TitleCrystal Structure of the second bromodomain of human Polybromo-1 (PB1) in complex with compound 16
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / Protein polybromo-1
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-Y8X / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsNunez, R. / Smith, B.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128840 United States
American Heart Association United States
CitationJournal: To Be Published
Title: Crystal Structure of the second bromodomain of human Polybromo-1 (PB1) in complex with compound 16
Authors: Nunez, R. / Smith, B.C.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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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)13,6354
Polymers13,2311
Non-polymers4043
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.657, 49.305, 33.544
Angle α, β, γ (deg.)90.000, 97.750, 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
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

21A-570-

HOH

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86U86
#2: Chemical ChemComp-Y8X / (2S)-5-chloro-2-(3-methylphenyl)-2,3-dihydroquinazolin-4(1H)-one


Mass: 272.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13ClN2O / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M MES pH 5.5, 14.4% PEG 8000, 10% Ethylene Glycol, 0.01M ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 25465 / % possible obs: 98.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.991 / Χ2: 0.048 / Net I/σ(I): 57.9 / Num. measured all: 54031
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.78-1.812.10.07812611.234195.8
1.81-1.8420.0712071.168196.6
1.84-1.882.10.06812861.294197.7
1.88-1.922.10.06412311.216197.6
1.92-1.962.10.06113131.242197.3
1.96-22.10.05811981.252198.1
2-2.052.10.05512981.168198.3
2.05-2.112.10.05412501.287198.7
2.11-2.172.10.05412651.259198.4
2.17-2.242.10.0513291.158199.2
2.24-2.322.10.04912281.13198.7
2.32-2.422.10.04912871.12199.6
2.42-2.532.10.04612841.051199.7
2.53-2.662.10.04712831.0761100
2.66-2.832.20.04313051.0611100
2.83-3.042.20.04412910.9781100
3.04-3.352.20.05112950.9621100
3.35-3.832.20.0712651.096199.8
3.83-4.832.20.06612931.067199.9
4.83-502.20.05212961.0871100

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Processing

Software
NameVersionClassification
PHENIXv1.20.1-4487refinement
CrystalCleardata collection
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→42.51 Å / SU ML: 0.1926 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 1322 9.99 %
Rwork0.1782 11906 -
obs0.181 13228 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.14 Å2
Refinement stepCycle: LAST / Resolution: 1.78→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 21 170 1122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079970
X-RAY DIFFRACTIONf_angle_d1.04321309
X-RAY DIFFRACTIONf_chiral_restr0.0529144
X-RAY DIFFRACTIONf_plane_restr0.0071165
X-RAY DIFFRACTIONf_dihedral_angle_d15.9749385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.850.29221460.23861312X-RAY DIFFRACTION99.32
1.85-1.940.25141450.1871314X-RAY DIFFRACTION100
1.94-2.040.19681470.16171312X-RAY DIFFRACTION100
2.04-2.170.1891450.17051316X-RAY DIFFRACTION100
2.17-2.330.20241470.16761325X-RAY DIFFRACTION99.86
2.33-2.570.19361470.16321312X-RAY DIFFRACTION100
2.57-2.940.19811470.17221323X-RAY DIFFRACTION100
2.94-3.70.21691490.17481339X-RAY DIFFRACTION99.93
3.7-42.510.20021490.1891353X-RAY DIFFRACTION99.73

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