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- PDB-6tlh: Crystal structure of mouse KANK3 ankyrin repeats -

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Basic information

Entry
Database: PDB / ID: 6tlh
TitleCrystal structure of mouse KANK3 ankyrin repeats
ComponentsKN motif and ankyrin repeat domain-containing protein 3
KeywordsCELL ADHESION / Protein binding / Ankyrin repeat domain-containing protein 47 / actin polymerization
Function / homology
Function and homology information


negative regulation of actin filament polymerization / negative regulation of stress fiber assembly / cytoskeleton / cytoplasm
Similarity search - Function
Kank N-terminal motif / KN motif / Domain of unknown function DUF3447 / 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
FORMIC ACID / KN motif and ankyrin repeat domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 mouse KANK3 ankyrin repeats
Authors: Khan, R. / Singh, A.K. / Goult, B.T.
History
DepositionDec 2, 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 3
B: KN motif and ankyrin repeat domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5978
Polymers54,0912
Non-polymers5066
Water6,666370
1
A: KN motif and ankyrin repeat domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1833
Polymers27,0451
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KN motif and ankyrin repeat domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4145
Polymers27,0451
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.437, 45.778, 69.596
Angle α, β, γ (deg.)90.000, 95.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-965-

HOH

21A-1090-

HOH

31B-946-

HOH

41B-1077-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A8 - 245
2111B8 - 245

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Components

#1: Protein KN motif and ankyrin repeat domain-containing protein 3 / Ankyrin repeat domain-containing protein 47


Mass: 27045.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 524-773 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kank3, Ankrd47, D17Ertd288e, Ng28 / Plasmid: pET-151-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z1P7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.19 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium formate, 20% 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: 1.8→69.32 Å / Num. obs: 42604 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2516 / CC1/2: 0.811 / Rpim(I) all: 0.472 / Rrim(I) all: 0.909 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hbd

4hbd


Resolution: 1.8→53.17 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.749 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.137
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 2143 5 %RANDOM
Rwork0.1994 ---
obs0.2012 40455 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130.28 Å2 / Biso mean: 32.084 Å2 / Biso min: 16.22 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å20.78 Å2
2---1.26 Å20 Å2
3---3.15 Å2
Refinement stepCycle: final / Resolution: 1.8→53.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 33 370 3940
Biso mean--43.91 38.4 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0153624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173251
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.734910
X-RAY DIFFRACTIONr_angle_other_deg0.5531.7557600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5875482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00422.086163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98315538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3511525
X-RAY DIFFRACTIONr_chiral_restr0.0730.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02594
Refine LS restraints NCSNumber: 1761 / Type: TIGHT THERMAL / Rms dev position: 4.13 Å / Weight position: 0.5
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 169 -
Rwork0.344 2956 -
all-3125 -
obs--96.66 %

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