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- PDB-5rji: PanDDA analysis group deposition of ground-state model of PHIP -

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Basic information

Entry
Database: PDB / ID: 5rji
TitlePanDDA analysis group deposition of ground-state model of PHIP
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 / insulin receptor binding / lysine-acetylated histone 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 / insulin receptor binding / lysine-acetylated histone binding / regulation of protein phosphorylation / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / 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
PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.24 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: 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


Theoretical massNumber of molelcules
Total (without water)17,6281
Polymers17,6281
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.712, 27.125, 55.930
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1698-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 1.73 Å3/Da / Density % sol: 28.91 % / 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.24→35.62 Å / Num. obs: 25085 / % possible obs: 72.8 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.013 / Rrim(I) all: 0.033 / Net I/σ(I): 29.8 / Num. measured all: 151965 / Scaling rejects: 362
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
1.24-1.281.70.1244132390.9730.1110.16749.1
5.41-35.626.20.02525904200.9990.0110.02853.291.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3MB3

3mb3


Resolution: 1.24→35.64 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.659 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 1257 5 %RANDOM
Rwork0.1655 ---
obs0.1666 23827 72.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.74 Å2 / Biso mean: 15.502 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.32 Å2
2--0.58 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.24→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 0 203 1193
Biso mean---28.4 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131058
X-RAY DIFFRACTIONr_bond_other_d0.0010.017958
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.6481436
X-RAY DIFFRACTIONr_angle_other_deg1.6771.5772234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0655129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.46921.45262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82515191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.438159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_mcbond_it1.2731.31504
X-RAY DIFFRACTIONr_mcbond_other1.2471.307503
X-RAY DIFFRACTIONr_mcangle_it1.8581.964637
LS refinement shellResolution: 1.241→1.274 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.151 11 -
Rwork0.212 210 -
all-221 -
obs--8.7 %

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