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- PDB-6tmd: Crystal structure of KANK2 ankyrin repeats mutant (A670V) -

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Basic information

Entry
Database: PDB / ID: 6tmd
TitleCrystal structure of KANK2 ankyrin repeats mutant (A670V)
ComponentsKN motif and ankyrin repeat domain-containing protein 2
KeywordsCELL ADHESION / Protein binding / ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 25 / MATRIX-REMODELING-ASSOCIATED PROTEIN 3
Function / homology
Function and homology information


negative regulation of vitamin D receptor signaling pathway / kidney epithelium development / podocyte cell migration / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of actin filament polymerization / regulation of Rho protein signal transduction / negative regulation of programmed cell death / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of cell population proliferation / apoptotic process ...negative regulation of vitamin D receptor signaling pathway / kidney epithelium development / podocyte cell migration / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of actin filament polymerization / regulation of Rho protein signal transduction / negative regulation of programmed cell death / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of cell population proliferation / apoptotic process / negative regulation of transcription by RNA polymerase II / mitochondrion / cytoplasm
Similarity search - Function
: / Kank N-terminal motif / KN motif / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
ACETATE ION / KN motif and ankyrin repeat domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKhan, R. / Singh, A.K. / Goult, B.T.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N007336/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBBS007245/1 United Kingdom
Human Frontier Science ProgramRGP00001/2016
CitationJournal: To be published
Title: Crystal structure of KANK2 ankyrin repeats mutant (A670V)
Authors: Khan, R. / Singh, A.K. / Goult, B.T.
History
DepositionDec 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: KN motif and ankyrin repeat domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5149
Polymers27,9431
Non-polymers5728
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-5 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.778, 45.659, 51.073
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1148-

HOH

21A-1175-

HOH

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Components

#1: Protein KN motif and ankyrin repeat domain-containing protein 2 / Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1- ...Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1-interacting protein / SRC1-interacting protein


Mass: 27942.971 Da / Num. of mol.: 1 / Mutation: Yes; A670V
Source method: isolated from a genetically manipulated source
Details: residues 583-832 / Source: (gene. exp.) Homo sapiens (human) / Gene: KANK2, ANKRD25, KIAA1518, MXRA3, SIP / Plasmid: PET-151-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q63ZY3
#2: 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
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.2 M ammonium acetate, 0.1 M Bis-tris pH 5.7, 31% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.5→47.15 Å / Num. obs: 35000 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 10.3
Reflection shellResolution: 1.5→1.521 Å / Redundancy: 3.2 % / Rmerge(I) obs: 2.239 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1775 / CC1/2: 0.329 / Rpim(I) all: 1.45 / Rrim(I) all: 2.674 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hbd

4hbd


Resolution: 1.5→47.15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.194 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.086
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1674 4.9 %RANDOM
Rwork0.1768 ---
obs0.1788 32838 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.95 Å2 / Biso mean: 27.083 Å2 / Biso min: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å20.5 Å2
2---1.49 Å2-0 Å2
3----1.1 Å2
Refinement stepCycle: final / Resolution: 1.5→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 38 186 2056
Biso mean--53.41 41.51 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131938
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171828
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6252634
X-RAY DIFFRACTIONr_angle_other_deg1.4721.5724235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1025255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50522.93592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11415330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1561512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022201
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02367
LS refinement shellResolution: 1.5→1.534 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.473 100 -
Rwork0.447 2070 -
obs--83.69 %

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