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- PDB-7bbo: Crystal Structure of the second bromodomain of Pleckstrin homolog... -

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Basic information

Entry
Database: PDB / ID: 7bbo
TitleCrystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group P212121
ComponentsPH-interacting protein
KeywordsPROTEIN BINDING / PHIP / PLECKSTRIN HOMOLOGY DOMAIN INTERACTING PROTEIN / bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / lysine-acetylated histone binding / insulin receptor binding / regulation of protein phosphorylation / insulin receptor signaling pathway ...regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / lysine-acetylated histone binding / insulin receptor binding / regulation of protein phosphorylation / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...: / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKrojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group P21212
Authors: Krojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: PH-interacting protein
BBB: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,99114
Polymers30,3122
Non-polymers67912
Water3,531196
1
AAA: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3204
Polymers15,1561
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,67110
Polymers15,1561
Non-polymers5159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.726, 56.477, 91.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PH-interacting protein / PHIP / DDB1- and CUL4-associated factor 14 / IRS-1 PH domain-binding protein / WD repeat-containing protein 11


Mass: 15156.185 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, DCAF14, WDR11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG6000 -- 10% ethylene glycol -- 0.1M tris pH 7.5 -- 0.1M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.32→56.48 Å / Num. obs: 59052 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 1.32→1.37 Å / Num. unique obs: 6528 / CC1/2: 0.577

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MB3

3mb3


Resolution: 1.32→48.148 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.161 / SU ML: 0.068 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2255 2843 4.829 %
Rwork0.1859 56025 -
all0.188 --
obs-58868 99.71 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.669 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å2-0 Å20 Å2
2---1.903 Å2-0 Å2
3----0.737 Å2
Refinement stepCycle: LAST / Resolution: 1.32→48.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 39 196 2267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132121
X-RAY DIFFRACTIONr_bond_other_d0.0140.0171976
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.662847
X-RAY DIFFRACTIONr_angle_other_deg1.6771.5794572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.5421.707123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72815383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1481517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022346
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02496
X-RAY DIFFRACTIONr_nbd_refined0.2220.2492
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21733
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21056
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2125
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.214
X-RAY DIFFRACTIONr_nbd_other0.210.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.226
X-RAY DIFFRACTIONr_mcbond_it2.3471.896988
X-RAY DIFFRACTIONr_mcbond_other2.3541.893987
X-RAY DIFFRACTIONr_mcangle_it3.0152.8521235
X-RAY DIFFRACTIONr_mcangle_other3.0182.8561236
X-RAY DIFFRACTIONr_scbond_it3.2612.4131133
X-RAY DIFFRACTIONr_scbond_other3.2612.4141134
X-RAY DIFFRACTIONr_scangle_it4.2083.4571612
X-RAY DIFFRACTIONr_scangle_other4.2073.4571613
X-RAY DIFFRACTIONr_lrange_it4.29523.6722522
X-RAY DIFFRACTIONr_lrange_other4.22223.3552477
X-RAY DIFFRACTIONr_rigid_bond_restr6.55734097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.3540.4152130.424019X-RAY DIFFRACTION98.648
1.354-1.3910.3962130.3943956X-RAY DIFFRACTION99.1675
1.391-1.4320.3711930.3583850X-RAY DIFFRACTION99.6058
1.432-1.4760.3951950.3313791X-RAY DIFFRACTION99.7248
1.476-1.5240.2861720.2553669X-RAY DIFFRACTION99.7403
1.524-1.5780.2731950.2313529X-RAY DIFFRACTION99.8927
1.578-1.6370.2691710.1973447X-RAY DIFFRACTION99.8896
1.637-1.7040.2611620.1763311X-RAY DIFFRACTION99.9137
1.704-1.7790.2271700.1543147X-RAY DIFFRACTION99.8495
1.779-1.8660.2421540.1493043X-RAY DIFFRACTION99.9062
1.866-1.9670.2361550.1622894X-RAY DIFFRACTION99.9672
1.967-2.0860.221310.1472764X-RAY DIFFRACTION100
2.086-2.230.1831110.142605X-RAY DIFFRACTION100
2.23-2.4080.1831160.1352436X-RAY DIFFRACTION99.9608
2.408-2.6380.2081070.1452251X-RAY DIFFRACTION99.9576
2.638-2.9480.1741120.152022X-RAY DIFFRACTION99.7196
2.948-3.4030.1891050.1691786X-RAY DIFFRACTION99.8416
3.403-4.1640.163610.1681558X-RAY DIFFRACTION99.6308
4.164-5.8730.191660.1731220X-RAY DIFFRACTION100
5.873-48.1480.268410.222727X-RAY DIFFRACTION99.4819

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