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- PDB-5rk5: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -

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Basic information

Entry
Database: PDB / ID: 5rk5
TitlePanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z57478994
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 / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / 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 / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / 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 / WD40 repeat, conserved site ...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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
5-(methoxymethyl)-1,3,4-thiadiazol-2-amine / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.243 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7732
Polymers17,6281
Non-polymers1451
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.659, 27.527, 55.667
Angle α, β, γ (deg.)90.000, 99.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1718-

HOH

21A-1817-

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-UVS / 5-(methoxymethyl)-1,3,4-thiadiazol-2-amine


Mass: 145.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.75 Å3/Da / Density % sol: 29.75 % / 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: 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: 1.24→27.47 Å / Num. obs: 26107 / % possible obs: 74.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 13.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.012 / Rrim(I) all: 0.03 / Net I/σ(I): 29.3 / Num. measured all: 153196 / Scaling rejects: 374
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
1.24-1.281.70.1054332510.9870.0950.1423.89.4
5.42-27.476.20.02326354230.9990.010.02557.491.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (29-NOV-2019)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3MB3

3mb3


Resolution: 1.243→27.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.068 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.063
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 1297 4.97 %RANDOM
Rwork0.1821 ---
obs0.1836 26105 75 %-
Displacement parametersBiso max: 65.42 Å2 / Biso mean: 20.12 Å2 / Biso min: 11.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.311 Å20 Å2-1.793 Å2
2---5.0931 Å20 Å2
3---3.782 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: final / Resolution: 1.243→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 9 223 1222
Biso mean--14.16 31.01 -
Num. residues----119
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d381SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes188HARMONIC5
X-RAY DIFFRACTIONt_it1059HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion135SEMIHARMONIC5
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_contact1333SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1059HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1436HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion16.02
LS refinement shellResolution: 1.24→1.29 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2318 27 5.16 %
Rwork0.1793 496 -
all-523 -
obs--12.91 %
Refinement TLS params.Method: refined / Origin x: -14.2334 Å / Origin y: 12.613 Å / Origin z: 12.8029 Å
111213212223313233
T-0.0248 Å20.0029 Å20.0059 Å2-0.0075 Å20.0089 Å2---0.0193 Å2
L0.3835 °20.0808 °2-0.1353 °2-0.2535 °2-0.0607 °2--1.1553 °2
S0.02 Å °0.0017 Å °-0.0009 Å °0.0051 Å °0.0314 Å °0.0297 Å °-0.0232 Å °-0.046 Å °-0.0513 Å °
Refinement TLS groupSelection details: { A|* }

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