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- PDB-5qho: PanDDA analysis group deposition of models with modelled events (... -

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Basic information

Entry
Database: PDB / ID: 5qho
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human FAM83B in complex with FMOPL000010a
ComponentsProtein FAM83B
KeywordsPROTEIN BINDING / PanDDA / SGC - Diamond I04-1 fragment screening / DUF1669 domain / XChemExplorer
Function / homology
Function and homology information


phosphatidylinositol 3-kinase catalytic subunit binding / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / epidermal growth factor receptor binding / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / Signaling by EGFR / cell population proliferation / protein kinase binding ...phosphatidylinositol 3-kinase catalytic subunit binding / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / epidermal growth factor receptor binding / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / Signaling by EGFR / cell population proliferation / protein kinase binding / signal transduction / membrane / cytoplasm / cytosol
Similarity search - Function
FAM83, N-terminal / : / Scaffolding anchor of CK1 domain / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
di(piperidin-1-yl)methanone / Protein FAM83B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.66 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. ...Pinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Bullock, A.N.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Authors: Pinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Bullock, A.N.
History
DepositionMay 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Protein FAM83B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1044
Polymers20,7831
Non-polymers3203
Water1,58588
1
A: Protein FAM83B
hetero molecules

A: Protein FAM83B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2078
Polymers41,5662
Non-polymers6416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z+3/41
Buried area3890 Å2
ΔGint-8 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.520, 50.520, 152.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Protein FAM83B


Mass: 20783.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM83B, C6orf143 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T0W9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOY / di(piperidin-1-yl)methanone


Mass: 196.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.58 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 27.3% Tacsimate pH 7.0, 0.15 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.66→50.48 Å / Num. obs: 24132 / % possible obs: 99.5 % / Redundancy: 8.1 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.02 / Rrim(I) all: 0.059 / Net I/σ(I): 13.7 / Num. measured all: 195256 / Scaling rejects: 22
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
1.66-1.76.82.0611189417440.5060.8242.2271100
7.42-50.487.20.022237632810.0090.02453.397.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LZK

5lzk


Resolution: 1.66→50.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.649 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 1256 5.3 %RANDOM
Rwork0.1978 ---
obs0.1998 22596 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.09 Å2 / Biso mean: 33.598 Å2 / Biso min: 18.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å2-0 Å2
2--0.56 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 1.66→50.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 22 88 1441
Biso mean--41.66 45.99 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191395
X-RAY DIFFRACTIONr_bond_other_d0.0020.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9511874
X-RAY DIFFRACTIONr_angle_other_deg1.0142.9763085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38422.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92715257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.776159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021513
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02296
X-RAY DIFFRACTIONr_mcbond_it2.8723.026664
X-RAY DIFFRACTIONr_mcbond_other2.8523.016663
X-RAY DIFFRACTIONr_mcangle_it4.0554.508830
LS refinement shellResolution: 1.658→1.701 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 85 -
Rwork0.397 1525 -
all-1610 -
obs--91.22 %

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