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- PDB-5ypx: Crystal structure of calaxin with magnesium -

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Basic information

Entry
Database: PDB / ID: 5ypx
TitleCrystal structure of calaxin with magnesium
ComponentsCalaxin
KeywordsMETAL BINDING PROTEIN / EF-hand / Calcium-binding protein / Neuronal calcium sensor / Calcium ion
Function / homology
Function and homology information


calcium-dependent outer dynein arm binding / regulation of flagellated sperm motility / cytoskeletal motor regulator activity / 9+2 motile cilium / dynein heavy chain binding / beta-tubulin binding / axoneme / cell chemotaxis / calcium ion binding
Similarity search - Function
Recoverin family / EF-hand domain pair / EF-hand, calcium binding motif / 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
Biological speciesCiona intestinalis (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsShojima, T. / Hou, F. / Takahashi, Y. / Okai, M. / Mizuno, K. / Inaba, K. / Miyakawa, T. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition
Authors: Shojima, T. / Hou, F. / Takahashi, Y. / Matsumura, Y. / Okai, M. / Nakamura, A. / Mizuno, K. / Inaba, K. / Kojima, M. / Miyakawa, T. / Tanokura, M.
History
DepositionNov 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Calaxin
B: Calaxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0797
Polymers51,9572
Non-polymers1225
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-33 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.258, 65.258, 113.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Calaxin


Mass: 25978.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: CALX, calx / Production host: Escherichia coli (E. coli) / References: UniProt: Q8T893
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: magnesium chloride, ammonium sulfate, PEG 5000 MME, barium chloride

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.836
11-H, K, -L20.164
ReflectionResolution: 2.64→46.1 Å / Num. obs: 14030 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→42.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.046 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21185 740 5.3 %RANDOM
Rwork0.16261 ---
obs0.16519 13256 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.64→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 5 21 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193087
X-RAY DIFFRACTIONr_bond_other_d0.0020.022975
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.984134
X-RAY DIFFRACTIONr_angle_other_deg1.03536893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67725.033153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25615620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023373
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02673
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4674.3251472
X-RAY DIFFRACTIONr_mcbond_other3.4664.3231471
X-RAY DIFFRACTIONr_mcangle_it5.4066.4731833
X-RAY DIFFRACTIONr_mcangle_other5.4056.4751834
X-RAY DIFFRACTIONr_scbond_it4.2534.7541615
X-RAY DIFFRACTIONr_scbond_other4.2514.7551616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7116.9452302
X-RAY DIFFRACTIONr_long_range_B_refined9.0433.5053584
X-RAY DIFFRACTIONr_long_range_B_other9.03833.523582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.637→2.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 59 -
Rwork0.214 969 -
obs--99.52 %

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