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- PDB-6wu7: Human Calcium and Integrin Binding Protein 3 E150Q K151H -

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Basic information

Entry
Database: PDB / ID: 6wu7
TitleHuman Calcium and Integrin Binding Protein 3 E150Q K151H
ComponentsCalcium and integrin-binding family member 3
KeywordsMETAL BINDING PROTEIN / EF-hand / Mechanotransduction / hearing
Function / homology
Function and homology information


calcium ion homeostasis / calcium ion binding / magnesium ion binding
Similarity search - Function
: / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
ACETATE ION / Calcium and integrin-binding family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsShapiro, L. / Dionne, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)5R01DC016960-03 United States
CitationJournal: Neuron / Year: 2021
Title: CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells.
Authors: Liang, X. / Qiu, X. / Dionne, G. / Cunningham, C.L. / Pucak, M.L. / Peng, G. / Kim, Y.H. / Lauer, A. / Shapiro, L. / Muller, U.
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: 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: Calcium and integrin-binding family member 3
B: Calcium and integrin-binding family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,13414
Polymers44,6342
Non-polymers50012
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The elution profile off of gel filtration had both monomer and dimer peaks.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-122 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.386, 84.386, 125.821
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-205-

CA

21B-410-

HOH

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Components

#1: Protein Calcium and integrin-binding family member 3 / Kinase-interacting protein 3 / KIP 3


Mass: 22317.143 Da / Num. of mol.: 2 / Mutation: E150Q, K151H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIB3, KIP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96Q77
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 8000 0.2M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.46 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.837→73.08 Å / Num. obs: 44453 / % possible obs: 96.93 % / Redundancy: 18 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Net I/σ(I): 42.15
Reflection shellResolution: 1.837→1.902 Å / Mean I/σ(I) obs: 7.12 / Num. unique obs: 3797 / CC1/2: 0.983 / % possible all: 84.12

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.18_3845refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WU5

6wu5


Resolution: 1.84→73.08 Å / SU ML: 0.1693 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1954 3793 4.48 %
Rwork0.1615 80900 -
obs0.163 84693 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.59 Å2
Refinement stepCycle: LAST / Resolution: 1.84→73.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 15 359 3370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00973078
X-RAY DIFFRACTIONf_angle_d1.08424173
X-RAY DIFFRACTIONf_chiral_restr0.0568448
X-RAY DIFFRACTIONf_plane_restr0.0072553
X-RAY DIFFRACTIONf_dihedral_angle_d22.2071141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.29061040.21562235X-RAY DIFFRACTION71.97
1.86-1.880.2511260.18422632X-RAY DIFFRACTION84.99
1.88-1.910.21611380.18912917X-RAY DIFFRACTION93.4
1.91-1.940.23871340.18282878X-RAY DIFFRACTION94.1
1.94-1.970.23151400.18312973X-RAY DIFFRACTION94.74
1.97-20.1981430.16942912X-RAY DIFFRACTION96.04
2-2.030.21671420.16993016X-RAY DIFFRACTION97.2
2.03-2.060.2211340.17743034X-RAY DIFFRACTION97.87
2.06-2.10.23441440.17493059X-RAY DIFFRACTION98.07
2.1-2.140.18751400.1673030X-RAY DIFFRACTION98.39
2.14-2.190.21371480.15583016X-RAY DIFFRACTION98.47
2.19-2.230.22571400.15383059X-RAY DIFFRACTION98.49
2.23-2.290.19571430.15863086X-RAY DIFFRACTION98.9
2.29-2.340.21141500.15493061X-RAY DIFFRACTION99.01
2.34-2.410.1781420.14773027X-RAY DIFFRACTION98.82
2.41-2.480.21751410.16373122X-RAY DIFFRACTION98.94
2.48-2.560.19121370.16053041X-RAY DIFFRACTION99.16
2.56-2.650.23291400.16313077X-RAY DIFFRACTION99.35
2.65-2.750.22541400.15693053X-RAY DIFFRACTION99.32
2.76-2.880.23841520.17033096X-RAY DIFFRACTION99.51
2.88-3.030.16371420.17133058X-RAY DIFFRACTION99.63
3.03-3.220.18611460.16963084X-RAY DIFFRACTION99.57
3.22-3.470.19011500.15393086X-RAY DIFFRACTION99.81
3.47-3.820.17631500.14653094X-RAY DIFFRACTION99.94
3.82-4.370.14181420.13733092X-RAY DIFFRACTION100
4.38-5.50.1541370.1453076X-RAY DIFFRACTION99.26
5.51-73.080.24131480.19653086X-RAY DIFFRACTION99.45

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