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- PDB-6wu5: Human Calcium and Integrin Binding Protein 3 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6wu5
TitleHuman Calcium and Integrin Binding Protein 3
ComponentsCalcium and integrin-binding family member 3
KeywordsMETAL BINDING PROTEIN / EF-hand / Dimer / NCS
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
THIOCYANATE ION / Calcium and integrin-binding family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDionne, G. / Shapiro, L.
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

Downloads & links

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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)45,17915
Polymers44,6182
Non-polymers56113
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes off of gel filtration columns with monomer and dimer eaks
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-139 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.752, 61.752, 180.969
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-380-

HOH

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Components

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


Mass: 22309.160 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.5 M Lithium Sulfate 0.2M Sodium Thiocyanate

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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: 1.879→60.32 Å / Num. obs: 33512 / % possible obs: 99.92 % / Redundancy: 18.3 % / Biso Wilson estimate: 37.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 34.59
Reflection shellResolution: 1.879→1.946 Å / Num. unique obs: 3270 / CC1/2: 0.901 / % possible all: 99.33

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXv1.18-3845-000refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xo5

1xo5


Resolution: 1.88→60.32 Å / SU ML: 0.1805 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7018
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2058 3733 5.95 %
Rwork0.1783 59006 -
obs0.1799 62739 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.36 Å2
Refinement stepCycle: LAST / Resolution: 1.88→60.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 21 154 3159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943068
X-RAY DIFFRACTIONf_angle_d0.80534151
X-RAY DIFFRACTIONf_chiral_restr0.047447
X-RAY DIFFRACTIONf_plane_restr0.0045547
X-RAY DIFFRACTIONf_dihedral_angle_d20.5781137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.31511350.30622061X-RAY DIFFRACTION96.44
1.9-1.930.32911420.27212246X-RAY DIFFRACTION99.79
1.93-1.950.25331300.23752158X-RAY DIFFRACTION99.69
1.95-1.980.2891400.22272211X-RAY DIFFRACTION99.75
1.98-2.010.2621400.21872174X-RAY DIFFRACTION99.7
2.01-2.040.23611320.22412172X-RAY DIFFRACTION99.91
2.04-2.080.26891280.20062161X-RAY DIFFRACTION100
2.08-2.110.28031380.19782199X-RAY DIFFRACTION99.66
2.11-2.150.1811420.20972185X-RAY DIFFRACTION100
2.15-2.190.23651460.18222217X-RAY DIFFRACTION99.75
2.19-2.240.20041420.17222177X-RAY DIFFRACTION99.96
2.24-2.290.21471420.17312208X-RAY DIFFRACTION100
2.29-2.340.19331420.18172138X-RAY DIFFRACTION99.91
2.34-2.40.22691360.17852202X-RAY DIFFRACTION99.91
2.4-2.460.20771360.17412200X-RAY DIFFRACTION99.91
2.46-2.530.21731280.17462187X-RAY DIFFRACTION100
2.53-2.620.23021330.19192194X-RAY DIFFRACTION100
2.62-2.710.19061360.18132202X-RAY DIFFRACTION99.91
2.71-2.820.20241520.1822228X-RAY DIFFRACTION100
2.82-2.950.2191340.18982161X-RAY DIFFRACTION100
2.95-3.10.19621420.20192187X-RAY DIFFRACTION99.96
3.1-3.30.19361360.17922192X-RAY DIFFRACTION100
3.3-3.550.21851420.16162186X-RAY DIFFRACTION99.96
3.55-3.910.18621340.16592201X-RAY DIFFRACTION100
3.91-4.470.16051490.14242187X-RAY DIFFRACTION100
4.48-5.630.17641400.1652195X-RAY DIFFRACTION100
5.64-60.320.24071360.19122177X-RAY DIFFRACTION99.74

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