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- PDB-6fd0: Human KIBRA C2 domain mutant M734I S735A -

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Basic information

Entry
Database: PDB / ID: 6fd0
TitleHuman KIBRA C2 domain mutant M734I S735A
ComponentsProtein KIBRA
KeywordsLIPID BINDING PROTEIN / C2 domain / Kibra / phosphoinositide-binding / membrane interaction
Function / homology
Function and homology information


regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / ruffle membrane / kinase binding / cell migration ...regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / ruffle membrane / kinase binding / cell migration / positive regulation of MAPK cascade / transcription coactivator activity / molecular adaptor activity / negative regulation of cell population proliferation / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
WWC, C2 domain / C2 domain / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...WWC, C2 domain / C2 domain / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein KIBRA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64215847029 Å
AuthorsCrennell, S.J. / Posner, M.G. / Bagby, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J008176/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain.
Authors: Posner, M.G. / Upadhyay, A. / Ishima, R. / Kalli, A.C. / Harris, G. / Kremerskothen, J. / Sansom, M.S.P. / Crennell, S.J. / Bagby, S.
History
DepositionDec 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,1116
Polymers31,7282
Non-polymers3824
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint2 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.240, 49.049, 49.549
Angle α, β, γ (deg.)62.708, 72.070, 83.709
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Protein KIBRA / HBeAg-binding protein 3 / Kidney and brain protein / KIBRA / WW domain-containing protein 1


Mass: 15864.071 Da / Num. of mol.: 2 / Fragment: C2 domain / Mutation: M734I S735A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWC1, KIAA0869 / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IX03
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.15M ammonium sulfate, 0.1M MES pH 6.0, 15% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 7811 / % possible obs: 98.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 57.8085399311 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.7
Reflection shellResolution: 2.62→2.67 Å / Redundancy: 3 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 333 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FB4

6fb4


Resolution: 2.64215847029→26.5563345923 Å / SU ML: 0.457856909525 / Cross valid method: FREE R-VALUE / σ(F): 1.96344096362 / Phase error: 36.6750307777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.29445628177 352 4.5197740113 %
Rwork0.206774170548 7436 -
obs0.210527740854 7788 97.691921726 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.8088730456 Å2
Refinement stepCycle: LAST / Resolution: 2.64215847029→26.5563345923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 25 2 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005193742976562105
X-RAY DIFFRACTIONf_angle_d0.7365469373842854
X-RAY DIFFRACTIONf_chiral_restr0.0470101865436337
X-RAY DIFFRACTIONf_plane_restr0.00303946211545361
X-RAY DIFFRACTIONf_dihedral_angle_d12.82761803551299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6422-3.0240.4076403472911150.3072445233062427X-RAY DIFFRACTION95.996978852
3.024-3.80820.3244145130951310.2212310437272522X-RAY DIFFRACTION99.2889221557
3.8082-26.55770.2461611114391060.1775161343082487X-RAY DIFFRACTION97.7752639517

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