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- PDB-7fv3: PanDDA analysis group deposition -- PHIP in complex with Z4912742924 -

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Basic information

Entry
Database: PDB / ID: 7fv3
TitlePanDDA analysis group deposition -- PHIP in complex with Z4912742924
ComponentsPH-interacting protein
KeywordsSIGNALING PROTEIN / False negatives / ligand features / rescreening / catalogue / fragment follow-ups / automated chemistry
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-ZKL / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.15 Å
AuthorsGrosjean, H. / Tomlinson, C. / Bradshaw, W.J. / Koekemoer, L. / Krojer, T. / Fearon, D. / Biggin, P.C. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustNone United Kingdom
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Grosjean, H. / Tomlinson, C. / Bradshaw, W.J. / Koekemoer, L. / Krojer, T. / Fearon, D. / Biggin, P.C. / von Delft, F.
History
DepositionMar 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,9212
Polymers17,6281
Non-polymers2931
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.800, 27.434, 56.297
Angle α, β, γ (deg.)90.000, 99.970, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2163-

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-ZKL / (2R)-N-butyl-4-(furan-2-carbonyl)-2-methylpiperazine-1-carboxamide


Mass: 293.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.76 Å3/Da / Density % sol: 30.3 % / 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: 0.92124 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.15→55.47 Å / Num. obs: 33187 / % possible obs: 75.4 % / Redundancy: 5.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.021 / Rrim(I) all: 0.051 / Net I/σ(I): 25.3 / Num. measured all: 174074 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique allNet I/σ(I) obs% possible allRmerge(I) obsCC1/2Rpim(I) allRrim(I) all
1.15-1.1711421411.36.1
6.09-55.475.7193634051.499.80.0830.9810.040.092

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7av9

7av9


Resolution: 1.15→55.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.131 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 1669 5 %RANDOM
Rwork0.179 ---
obs0.1795 31518 75.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.36 Å2 / Biso mean: 20.443 Å2 / Biso min: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20.21 Å2
2--1.15 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.15→55.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms995 0 21 169 1185
Biso mean--38.78 27.74 -
Num. residues----120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0153329
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142178
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.6753265
X-RAY DIFFRACTIONr_angle_other_deg1.4151.5865088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.17320.507138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23515405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6521521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022788
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02572
X-RAY DIFFRACTIONr_mcbond_it1.4971.9781621
X-RAY DIFFRACTIONr_mcbond_other1.5561.8741497
X-RAY DIFFRACTIONr_mcangle_it3.0332.711447
LS refinement shellResolution: 1.151→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 17 -
Rwork0.327 236 -
all-253 -
obs--7.82 %

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