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- PDB-5s9j: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -

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Basic information

Entry
Database: PDB / ID: 5s9j
TitlePanDDA analysis group deposition -- Crystal Structure of PHIP in complex with starting material
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 / 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, 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
2-azanyl-3-methyl-benzoic acid / 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)17,7792
Polymers17,6281
Non-polymers1511
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.446, 26.757, 55.808
Angle α, β, γ (deg.)90.000, 100.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1720-

HOH

21A-1793-

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-3M0 / 2-azanyl-3-methyl-benzoic acid / 3-methylanthranilate


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.7 Å3/Da / Density % sol: 27.51 % / 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: 0.9127 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9127 Å / Relative weight: 1
ReflectionResolution: 1.15→54.91 Å / Num. obs: 35016 / % possible obs: 82.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 13.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.036 / Rrim(I) all: 0.065 / Net I/σ(I): 8.2 / Num. measured all: 94019 / Scaling rejects: 28
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
1.15-1.171.21.0987145970.2131.0981.5530.428.8
6.3-54.9130.0298762930.9980.0190.03526.299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (18-SEP-2020)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5RJI

5rji


Resolution: 1.15→54.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.056 / SU Rfree Blow DPI: 0.056 / SU Rfree Cruickshank DPI: 0.052
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1776 5.08 %RANDOM
Rwork0.2059 ---
obs0.2068 34991 82.3 %-
Displacement parametersBiso max: 108.98 Å2 / Biso mean: 18.6 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.5374 Å20 Å2-1.9491 Å2
2---2.1185 Å20 Å2
3---2.6558 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: final / Resolution: 1.15→54.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 11 200 1201
Biso mean--16.26 29.33 -
Num. residues----119
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d376SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes189HARMONIC5
X-RAY DIFFRACTIONt_it1052HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion133SEMIHARMONIC5
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_contact1447SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1052HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1426HARMONIC20.84
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion12.86
LS refinement shellResolution: 1.15→1.17 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2877 42 6 %
Rwork0.2413 658 -
all-700 -
obs--29.37 %
Refinement TLS params.Method: refined / Origin x: -14.2209 Å / Origin y: 12.3551 Å / Origin z: 12.6226 Å
111213212223313233
T-0.0079 Å20.0088 Å2-0.002 Å2--0.0055 Å20.0066 Å2---0.0106 Å2
L0.4881 °20.1456 °2-0.5328 °2-0.2633 °20.0932 °2--0.767 °2
S0.0107 Å °0.0633 Å °0.0167 Å °0.0881 Å °0.0152 Å °0.0128 Å °-0.0048 Å °0.0346 Å °-0.0259 Å °
Refinement TLS groupSelection details: { A|* }

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