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- PDB-5lzk: Structure of the domain of unknown function DUF1669 from human FAM83B -

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Basic information

Entry
Database: PDB / ID: 5lzk
TitleStructure of the domain of unknown function DUF1669 from human FAM83B
ComponentsProtein FAM83B
KeywordsSTRUCTURAL GENOMICS / domain of unknown function / Structural Genomics Consortium / SGC
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
IODIDE ION / Protein FAM83B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.575 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Williams, E.P. / Shrestha, L. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106169/ZZ14/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of the domain of unknown function DUF1669 from human FAM83B
Authors: Pinkas, D.M. / Bufton, J.C. / Williams, E.P. / Shrestha, L. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionSep 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FAM83B
B: Protein FAM83B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,50813
Polymers41,5662
Non-polymers94211
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint6 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.498, 73.959, 63.081
Angle α, β, γ (deg.)90.00, 96.19, 90.00
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 / Fragment: UNP residues 117-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM83B, C6orf143 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5T0W9
#2: Chemical
ChemComp-IOD / IODIDE ION


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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 29% PEG3350 0.1M bis-tris-propane pH 8.0 0.2M sodium iodide 10% ethylene glycol

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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 2M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.575→47.832 Å / Num. obs: 46738 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.2
Reflection shellResolution: 1.575→1.581 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / CC1/2: 0.716 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.9_1682refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4URJ

4urj


Resolution: 1.575→47.832 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21
RfactorNum. reflection% reflection
Rfree0.1889 2305 4.94 %
Rwork0.1595 --
obs0.1609 46699 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.575→47.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 32 280 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122851
X-RAY DIFFRACTIONf_angle_d1.2923828
X-RAY DIFFRACTIONf_dihedral_angle_d13.781069
X-RAY DIFFRACTIONf_chiral_restr0.065430
X-RAY DIFFRACTIONf_plane_restr0.006475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5753-1.60960.28291410.25572779X-RAY DIFFRACTION100
1.6096-1.6470.26721330.24262818X-RAY DIFFRACTION100
1.647-1.68820.28361490.23472778X-RAY DIFFRACTION100
1.6882-1.73390.27431390.22612792X-RAY DIFFRACTION100
1.7339-1.78490.26621430.20222838X-RAY DIFFRACTION100
1.7849-1.84250.1961350.18132777X-RAY DIFFRACTION100
1.8425-1.90830.22211470.17442794X-RAY DIFFRACTION100
1.9083-1.98480.21941540.16262332X-RAY DIFFRACTION83
1.9848-2.07510.16611260.15232811X-RAY DIFFRACTION100
2.0751-2.18450.1771530.14772779X-RAY DIFFRACTION100
2.1845-2.32130.19861400.14062817X-RAY DIFFRACTION100
2.3213-2.50060.16841470.1382813X-RAY DIFFRACTION100
2.5006-2.75220.18061680.1462778X-RAY DIFFRACTION100
2.7522-3.15040.17981450.14512827X-RAY DIFFRACTION100
3.1504-3.96880.16531500.14132807X-RAY DIFFRACTION100
3.9688-47.85410.16291350.15412854X-RAY DIFFRACTION99

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