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- PDB-5s8d: XChem group deposition -- Crystal Structure of the second bromodo... -

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Basic information

Entry
Database: PDB / ID: 5s8d
TitleXChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N00539e (space group C2)
ComponentsPH-interacting protein
KeywordsSIGNALING PROTEIN / SGC - Diamond I04-1 fragment screening / bromodomain / PHIP / XChemExplorer
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
methyl quinoline-6-carboxylate / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.26 Å
AuthorsKrojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F.
CitationJournal: To Be Published
Title: XChem group deposition
Authors: Krojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 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)15,3432
Polymers15,1561
Non-polymers1871
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.850, 27.520, 56.640
Angle α, β, γ (deg.)90.000, 100.250, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1715-

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: 15156.185 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-N1E / methyl quinoline-6-carboxylate


Mass: 187.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.1 Å3/Da / Density % sol: 41.32 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.04M potassium phosphate monobasic -- 11% PEG8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.26→40.76 Å / Num. obs: 33081 / % possible obs: 96.2 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.023 / Rrim(I) all: 0.042 / Net I/σ(I): 16.8 / Num. measured all: 93367 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.26-1.2920.789464123420.5390.6691.0391.292.9
5.64-40.762.90.012123442110.0080.01565.597.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7AV9

7av9


Resolution: 1.26→40.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.792 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 1638 5 %RANDOM
Rwork0.1749 ---
obs0.1767 31439 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.26 Å2 / Biso mean: 18.052 Å2 / Biso min: 10.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å21.54 Å2
2---0.43 Å20 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 1.26→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 14 116 1120
Biso mean--28.45 27.04 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131062
X-RAY DIFFRACTIONr_bond_other_d0.0050.017963
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6481439
X-RAY DIFFRACTIONr_angle_other_deg1.5571.582232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.66121.45262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78815188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.156159
X-RAY DIFFRACTIONr_chiral_restr0.110.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021210
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02259
X-RAY DIFFRACTIONr_mcbond_it2.0261.617499
X-RAY DIFFRACTIONr_mcbond_other1.9628.42498
X-RAY DIFFRACTIONr_mcangle_it2.2232.43629
X-RAY DIFFRACTIONr_rigid_bond_restr3.14132022
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 142 -
Rwork0.36 2199 -
all-2341 -
obs--92.79 %

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