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- PDB-6fde: Crystal Structure of the HHD2 Domain of Whirlin : 3-helix conformation -

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Basic information

Entry
Database: PDB / ID: 6fde
TitleCrystal Structure of the HHD2 Domain of Whirlin : 3-helix conformation
ComponentsWhirlin
KeywordsSTRUCTURAL PROTEIN / Usher syndrome / scaffold protein / hearing / deafness
Function / homology
Function and homology information


axon collateral / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium ...axon collateral / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium / stereocilium tip / inner ear receptor cell stereocilium organization / detection of mechanical stimulus involved in sensory perception of sound / stereocilium bundle / stereocilium / apical dendrite / retina homeostasis / auditory receptor cell stereocilium organization / photoreceptor inner segment / ciliary basal body / dendritic shaft / establishment of localization in cell / actin filament / sensory perception of sound / establishment of protein localization / cilium / presynapse / growth cone / postsynapse / neuron projection / protein domain specific binding / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Whirlin / : / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDelhommel, F. / Cordier, F. / Saul, F. / Haouz, A. / Wolff, N.
Funding support France, 3items
OrganizationGrant numberCountry
Fondation de France-Committee Berthe Fouassier France
Institut Pasteur France
Ministere de l'Enseignement Superieur et de la Recherche France
CitationJournal: FEBS J. / Year: 2018
Title: Structural plasticity of the HHD2 domain of whirlin.
Authors: Delhommel, F. / Cordier, F. / Saul, F. / Chataigner, L. / Haouz, A. / Wolff, N.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Whirlin


Theoretical massNumber of molelcules
Total (without water)9,6821
Polymers9,6821
Non-polymers00
Water18010
1
A: Whirlin

A: Whirlin


Theoretical massNumber of molelcules
Total (without water)19,3642
Polymers19,3642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2090 Å2
ΔGint-25 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.668, 34.668, 99.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Whirlin


Mass: 9682.091 Da / Num. of mol.: 1 / Fragment: WHIRLIN DOMAIN HHD2 RESIDUES 420-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Whrn, Dfnb31, Kiaa1526 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80VW5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.6 Å3/Da / Density % sol: 20.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na cit 2-propanolOH 20% w/vPEG4K 20% w:v

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→34.67 Å / Num. obs: 5620 / % possible obs: 98.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 33.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.03 / Net I/σ(I): 15.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 314 / CC1/2: 0.376 / Rpim(I) all: 0.389 / % possible all: 92.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→32.75 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.257 550 9.85 %RANDOM
Rwork0.214 ---
obs0.219 5583 98.3 %-
Displacement parametersBiso mean: 41.32 Å2
Baniso -1Baniso -2Baniso -3
1--4.0786 Å20 Å20 Å2
2---4.0786 Å20 Å2
3---8.1573 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 1.85→32.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms538 0 0 10 548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01562HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.91762HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d201SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes11HARMONIC2
X-RAY DIFFRACTIONt_gen_planes85HARMONIC5
X-RAY DIFFRACTIONt_it562HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion16.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion75SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact663SEMIHARMONIC4
LS refinement shellResolution: 1.85→2.07 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2467 147 9.77 %
Rwork0.2242 1357 -
all0.2263 1504 -
obs--96.66 %
Refinement TLS params.Method: refined / Origin x: 5.8468 Å / Origin y: 13.784 Å / Origin z: 2.701 Å
111213212223313233
T0.0487 Å20.0372 Å2-0.039 Å2--0.0452 Å2-0.0453 Å2--0.0314 Å2
L2.6185 °2-0.9623 °22.2406 °2-2.299 °2-2.4673 °2--5.0504 °2
S-0.182 Å °-0.0752 Å °0.2888 Å °0.0366 Å °-0.029 Å °-0.181 Å °-0.0753 Å °-0.2009 Å °0.211 Å °
Refinement TLS groupSelection details: { A|* }

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