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

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Basic information

Entry
Database: PDB / ID: 5qhl
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human FAM83B in complex with FMOPL000551a
ComponentsProtein FAM83B
KeywordsPROTEIN BINDING / PanDDA / SGC - Diamond I04-1 fragment screening / DUF1669 domain / XChemExplorer
Function / homology
Function and homology information


protein localization to mitotic spindle / keratin filament / keratin filament binding / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cell cycle G1/S phase transition / intermediate filament cytoskeleton organization / regulation of TOR signaling / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / RND2 GTPase cycle ...protein localization to mitotic spindle / keratin filament / keratin filament binding / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cell cycle G1/S phase transition / intermediate filament cytoskeleton organization / regulation of TOR signaling / 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 / mitotic spindle pole / BMP signaling pathway / regulation of ERK1 and ERK2 cascade / epidermal growth factor receptor signaling pathway / cell population proliferation / positive regulation of cell migration / protein kinase binding / signal transduction / membrane / nucleus / 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
[5-(4-aminophenyl)furan-2-yl]methanol / IODIDE ION / Protein FAM83B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.68 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 1.1Mar 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: Protein FAM83B
B: Protein FAM83B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,76313
Polymers41,5662
Non-polymers1,19611
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-6 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.730, 74.390, 63.160
Angle α, β, γ (deg.)90.000, 96.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein FAM83B


Mass: 20783.109 Da / Num. of mol.: 2
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-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GQ7 / [5-(4-aminophenyl)furan-2-yl]methanol


Mass: 189.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.12 Å3/Da / Density % sol: 41.94 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M NaP monobasic, 0.8M KP dibasic, 0.1M HEPES pH 7.5 5%(w/v) PEG10K

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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: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.68→47.96 Å / Num. obs: 39230 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.062 / Rrim(I) all: 0.114 / Net I/σ(I): 7.5 / Num. measured all: 131307 / Scaling rejects: 0
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
1.68-1.723.31.275964829070.4940.8241.523199.6
7.51-47.963.40.0314894320.9980.0190.03629.293.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LZK

5lzk


Resolution: 1.68→62.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.502 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1886 4.8 %RANDOM
Rwork0.1706 ---
obs0.1728 37322 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 215.51 Å2 / Biso mean: 28.065 Å2 / Biso min: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å2-0 Å2-0.09 Å2
2---1.69 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.68→62.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 52 276 3073
Biso mean--42.04 46.95 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023202
X-RAY DIFFRACTIONr_bond_other_d0.0020.022882
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9664127
X-RAY DIFFRACTIONr_angle_other_deg1.0536660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21122.707133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53915557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2631523
X-RAY DIFFRACTIONr_chiral_restr0.1280.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023645
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02694
X-RAY DIFFRACTIONr_mcbond_it2.2312.441500
X-RAY DIFFRACTIONr_mcbond_other2.2312.441500
X-RAY DIFFRACTIONr_mcangle_it3.2463.631828
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 143 -
Rwork0.344 2758 -
all-2901 -
obs--99.59 %

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