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- PDB-5s97: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -

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Basic information

Entry
Database: PDB / ID: 5s97
TitlePanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative
ComponentsPH-interacting protein
KeywordsSIGNALING PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / Robotic chemistry / Crystal soaking / Reaction crudes
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
Chem-Y2V / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.15 Å
AuthorsGrosjean, H. / Aimon, A. / Hassel-Hart , S. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Biggin, P.C. / Spencer, J. / von Delft, F.
CitationJournal: To Be Published
Title: Crystal Structures of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group C2 soaked with crude reaction mixtures
Authors: Grosjean, H. / Aimon, A. / Hart , S. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Biggin, P.C. / Spencer, J. / von Delft, F.
History
DepositionJan 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9472
Polymers17,6281
Non-polymers3191
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.425, 27.154, 55.903
Angle α, β, γ (deg.)90.000, 100.370, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1668-

HOH

21A-1792-

HOH

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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: 17627.859 Da / Num. of mol.: 1
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-Y2V / 4-(5-methylfuran-2-carbonyl)-N-(2,2,2-trifluoroethyl)piperazine-1-carboxamide


Mass: 319.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16F3N3O3
#3: Water ChemComp-HOH / water


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

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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: 1.72 Å3/Da / Density % sol: 28.67 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 8000, 0.04M POTASSIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9126 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9126 Å / Relative weight: 1
ReflectionResolution: 1.15→54.99 Å / Num. obs: 37258 / % possible obs: 86.3 % / Redundancy: 2.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.044 / Rrim(I) all: 0.079 / Net I/σ(I): 7.1 / Num. measured all: 92996 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.15-1.1710.5126306130.7170.5120.7240.629.3
6.3-54.992.90.0678742980.990.0460.08217.199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5RJI

5rji


Resolution: 1.15→54.99 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.29 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 1843 5 %RANDOM
Rwork0.1772 ---
obs0.1787 35054 85.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.08 Å2 / Biso mean: 15.571 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.25 Å2
2--0.77 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 1.15→54.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 22 196 1208
Biso mean--11.98 27.53 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0142388
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171637
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.6582556
X-RAY DIFFRACTIONr_angle_other_deg1.5261.6093841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.69921.963107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9115312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4881515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022298
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02436
X-RAY DIFFRACTIONr_mcbond_it0.8751.4281124
X-RAY DIFFRACTIONr_mcbond_other0.8821.4141107
X-RAY DIFFRACTIONr_mcangle_it1.4892.0941137
LS refinement shellResolution: 1.15→1.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.517 38 -
Rwork0.464 841 -
all-879 -
obs--27.69 %

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