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- PDB-5rk4: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -

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Basic information

Entry
Database: PDB / ID: 5rk4
TitlePanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z56791867
ComponentsPH-interacting protein
KeywordsPROTEIN BINDING / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / Fragment-based drug design / SAMPL7
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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily ...: / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-K1S / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.284 Å
AuthorsGrosjean, H. / Aimon, A. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Biggin, P.C.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of ground-state model
Authors: Grosjean, H. / Aimon, A. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Biggin, P.C.
History
DepositionJun 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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)17,8332
Polymers17,6281
Non-polymers2051
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)81.598, 27.322, 55.985
Angle α, β, γ (deg.)90.000, 99.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1788-

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-K1S / N,N-diethyl-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-amine


Mass: 205.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.74 Å3/Da / Density % sol: 29.45 %
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: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.287→40.184 Å / Num. obs: 25960 / % possible obs: 85.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 13.74 Å2 / CC1/2: 1 / Rpim(I) all: 0.011 / Rrim(I) all: 0.029 / Net I/σ(I): 29.6 / Num. measured all: 149835
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.287-1.3463.1409012990.9650.1610.3033.136.3
3.737-40.1846.2804312970.9990.010.02573.795.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (29-NOV-2019)refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3MB3

3mb3


Resolution: 1.284→40.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.07 / SU Rfree Cruickshank DPI: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1302 5.01 %RANDOM
Rwork0.1967 ---
obs0.1979 25974 82.5 %-
Displacement parametersBiso max: 73.41 Å2 / Biso mean: 18.09 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.2789 Å20 Å20.1001 Å2
2--0.9532 Å20 Å2
3----0.6744 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: final / Resolution: 1.284→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 15 196 1201
Biso mean--20.33 28.37 -
Num. residues----118
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d381SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes196HARMONIC5
X-RAY DIFFRACTIONt_it1064HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion134SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1354SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1064HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg1444HARMONIC20.84
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion14.62
LS refinement shellResolution: 1.28→1.31 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.284 31 5.96 %
Rwork0.2072 489 -
all-520 -
obs--24.83 %
Refinement TLS params.Method: refined / Origin x: -14.3462 Å / Origin y: 12.4802 Å / Origin z: 12.7945 Å
111213212223313233
T-0.0142 Å20.0083 Å20.0026 Å2--0.0075 Å20.0001 Å2---0.0246 Å2
L0.9255 °20.0234 °2-0.7275 °2-0.5457 °20.1669 °2--1.1282 °2
S0.0093 Å °-0.0192 Å °0.0233 Å °0.0827 Å °0.0149 Å °0.0179 Å °-0.0206 Å °0.0463 Å °-0.0242 Å °
Refinement TLS groupSelection details: { A|* }

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