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- PDB-5fh8: Crystal structure of the fifth bromodomain of human PB1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5fh8
TitleCrystal structure of the fifth bromodomain of human PB1 in complex with compound 28
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PBRM1 / BRG1-associated factor 180 / chromatin remodeling
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 T cell differentiation / positive regulation of double-strand break repair / 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 T cell differentiation / positive regulation of double-strand break repair / 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 / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5XK / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTallant, C. / Sutherell, C.L. / Siejka, P. / Sorrell, F.J. / Krojer, T. / Picaud, S. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Tallant, C. / Sutherell, C.L. / Siejka, P. / Sorrell, F.J. / Krojer, T. / Picaud, S. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Ley, S.V. / Knapp, S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex.
Authors: Sutherell, C.L. / Tallant, C. / Monteiro, O.P. / Yapp, C. / Fuchs, J.E. / Fedorov, O. / Siejka, P. / Muller, S. / Knapp, S. / Brenton, J.D. / Brennan, P.E. / Ley, S.V.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Protein polybromo-1
B: Protein polybromo-1
C: Protein polybromo-1
D: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,94310
Polymers58,5924
Non-polymers1,3516
Water4,630257
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0293
Polymers14,6481
Non-polymers3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9512
Polymers14,6481
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9512
Polymers14,6481
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0133
Polymers14,6481
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.580, 62.420, 65.820
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U86
#2: Chemical
ChemComp-5XK / 6-chloranyl-3-(2-ethylbutyl)-4~{H}-pyrrolo[1,2-a]quinazolin-5-one


Mass: 302.799 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H19ClN2O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% MPD, 0.1 M bicine pH 9 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.55→64.55 Å / Num. all: 68763 / Num. obs: 68763 / % possible obs: 90.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.3
Reflection shellResolution: 1.55→6.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.5 / % possible all: 52.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q0O

4q0o


Resolution: 1.55→64.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.376 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22401 3423 5 %RANDOM
Rwork0.18731 ---
obs0.1891 65305 90.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20.18 Å2
2---0.14 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.55→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 92 257 4037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193875
X-RAY DIFFRACTIONr_bond_other_d0.0020.023768
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9915215
X-RAY DIFFRACTIONr_angle_other_deg1.01238691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0795445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3923.622185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05315763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1371533
X-RAY DIFFRACTIONr_chiral_restr0.1120.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02861
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5152.2321768
X-RAY DIFFRACTIONr_mcbond_other1.5142.2321769
X-RAY DIFFRACTIONr_mcangle_it2.3083.3322205
X-RAY DIFFRACTIONr_mcangle_other2.3073.3352206
X-RAY DIFFRACTIONr_scbond_it2.4542.6112107
X-RAY DIFFRACTIONr_scbond_other2.4542.6122108
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.883.7593007
X-RAY DIFFRACTIONr_long_range_B_refined5.44418.3744631
X-RAY DIFFRACTIONr_long_range_B_other5.41318.114528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 142 -
Rwork0.299 2757 -
obs--51.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.55070.0252-0.11010.25280.11330.0809-0.01710.024-0.0082-0.0030.024-0.03530.0020.0005-0.00690.02360.00790.01680.0144-0.00930.0345Chain A9.125320.18694.6022
20.272-0.0720.1350.7685-0.27810.20680.02940.0346-0.0227-0.03110.03620.12620.0310.01-0.06560.00870.0029-0.00310.01550.00870.0397Chain B21.35741.394736.4974
30.7681-0.01190.26310.5829-0.12540.60610.0889-0.0960.01920.0317-0.08360.15260.1010.0333-0.00530.0353-0.00370.02460.0311-0.01830.0515Chain C-8.459212.6220.6864
41.36070.67440.3710.63410.21580.229-0.15230.04480.2465-0.0670.08780.16950.00520.02050.06450.0343-0.0023-0.03120.01690.01210.0879Chain D24.455240.070212.1161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D654 - 762
2X-RAY DIFFRACTION2B653 - 763
3X-RAY DIFFRACTION3C654 - 762
4X-RAY DIFFRACTION4D654 - 762

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