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

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Basic information

Entry
Database: PDB / ID: 5qhs
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human FAM83B in complex with FF000014a
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 / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / cell population proliferation / protein kinase binding ...phosphatidylinositol 3-kinase catalytic subunit binding / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / cell population proliferation / protein kinase binding / signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
FAM83, N-terminal / : / FAM83 A-H / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-methyl-3-oxidanyl-pyridin-2-one / Protein FAM83B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.95 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 30, 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)21,0324
Polymers20,7831
Non-polymers2493
Water1,63991
1
A: Protein FAM83B
hetero molecules

A: Protein FAM83B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0658
Polymers41,5662
Non-polymers4996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z+3/41
Buried area3860 Å2
ΔGint-5 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.774, 50.774, 154.078
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-GQV / 1-methyl-3-oxidanyl-pyridin-2-one


Mass: 125.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.39 Å3/Da / Density % sol: 48.51 % / 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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→51.41 Å / Num. obs: 15563 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.033 / Rrim(I) all: 0.116 / Net I/σ(I): 14 / Num. measured all: 188277 / Scaling rejects: 82
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
1.95-211.61.1691288111060.5090.3561.2232.3100
8.72-51.418.80.0320932380.9990.010.03243.599.9

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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: 1.95→50.77 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.486 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 810 5.3 %RANDOM
Rwork0.203 ---
obs0.2056 14351 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 34.551 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å2-0 Å2
2--0.61 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: final / Resolution: 1.95→50.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 17 92 1440
Biso mean--45.63 44.43 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191382
X-RAY DIFFRACTIONr_bond_other_d0.0020.021306
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9531854
X-RAY DIFFRACTIONr_angle_other_deg0.99333018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44123.43864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95815256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.124159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021532
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02298
X-RAY DIFFRACTIONr_mcbond_it2.9643.149660
X-RAY DIFFRACTIONr_mcbond_other2.9623.15661
X-RAY DIFFRACTIONr_mcangle_it4.1584.683822
LS refinement shellResolution: 1.948→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 69 -
Rwork0.353 946 -
all-1015 -
obs--91.86 %

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