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- PDB-7wej: Crystal structure of the mouse Wdr47 NTD. -

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Basic information

Entry
Database: PDB / ID: 7wej
TitleCrystal structure of the mouse Wdr47 NTD.
ComponentsWD repeat-containing protein 47
KeywordsPROTEIN BINDING / LisH motif containing protein
Function / homology
Function and homology information


microtubule / cytoplasm
Similarity search - Function
WD repeat-containing protein 47 / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / WD40 repeat, conserved site ...WD repeat-containing protein 47 / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing protein 47
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.09 Å
AuthorsRen, J.Q. / Li, D. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Rep / Year: 2022
Title: Intertwined Wdr47-NTD dimer recognizes a basic-helical motif in Camsap proteins for proper central-pair microtubule formation.
Authors: Ren, J. / Li, D. / Liu, J. / Liu, H. / Yan, X. / Zhu, X. / Feng, W.
History
DepositionDec 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 47
B: WD repeat-containing protein 47


Theoretical massNumber of molelcules
Total (without water)73,1012
Polymers73,1012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, the molar mass was calculated by SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-88 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.384, 75.762, 170.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein WD repeat-containing protein 47 / Neuronal enriched MAP interacting protein / Nemitin


Mass: 36550.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wdr47, Kiaa0893 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CGF6
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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 8% (v/v) Tacsimate pH 7.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 25839 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 96.28 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.035 / Rrim(I) all: 0.094 / Χ2: 0.476 / Net I/σ(I): 13.1
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 2601 / CC1/2: 0.808 / CC star: 0.945 / Rpim(I) all: 0.378 / Rrim(I) all: 0.954 / Χ2: 0.433 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIXv1.18refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
PDB_EXTRACT3.27data extraction
Cootv0.8.9.2model building
RefinementMethod to determine structure: SAD / Resolution: 3.09→37.88 Å / SU ML: 0.531 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.29 2573 9.98 %
Rwork0.256 23198 -
obs0.2593 25771 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.3 Å2
Refinement stepCycle: LAST / Resolution: 3.09→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4170 0 0 0 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00174248
X-RAY DIFFRACTIONf_angle_d0.42265734
X-RAY DIFFRACTIONf_chiral_restr0.0345677
X-RAY DIFFRACTIONf_plane_restr0.0031718
X-RAY DIFFRACTIONf_dihedral_angle_d12.68751553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.150.53651440.4211277X-RAY DIFFRACTION94.92
3.15-3.210.41881370.4071226X-RAY DIFFRACTION94.39
3.21-3.280.43221360.34671231X-RAY DIFFRACTION93.06
3.28-3.360.37781480.32371324X-RAY DIFFRACTION99.93
3.36-3.440.33361410.31241299X-RAY DIFFRACTION99.52
3.44-3.540.30931470.2791297X-RAY DIFFRACTION100
3.54-3.640.32731470.29171303X-RAY DIFFRACTION99.59
3.64-3.760.32851490.28371307X-RAY DIFFRACTION100
3.76-3.890.31021480.27471300X-RAY DIFFRACTION99.72
3.89-4.050.30851440.25611339X-RAY DIFFRACTION99.93
4.05-4.230.30921360.23661270X-RAY DIFFRACTION99.5
4.23-4.450.20161500.23281345X-RAY DIFFRACTION99.47
4.45-4.730.27291350.22631232X-RAY DIFFRACTION93.89
4.73-5.10.27271430.21721276X-RAY DIFFRACTION97.13
5.1-5.610.30281460.25091301X-RAY DIFFRACTION99.93
5.61-6.420.33331440.28431319X-RAY DIFFRACTION99.66
6.42-8.070.24331470.25631301X-RAY DIFFRACTION99.38
8.08-37.880.24641310.21431251X-RAY DIFFRACTION95.31

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