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- PDB-7clt: Crystal structure of the EFhd1/Swiprosin-2, a mitochondrial actin... -

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Basic information

Entry
Database: PDB / ID: 7clt
TitleCrystal structure of the EFhd1/Swiprosin-2, a mitochondrial actin-binding protein
ComponentsEF-hand domain-containing protein D1
KeywordsMETAL BINDING PROTEIN / mitochondria / calcium-binding
Function / homology
Function and homology information


regulation of cellular hyperosmotic salinity response / calcium ion sensor activity / neuron projection development / mitochondrial inner membrane / calcium ion binding / mitochondrion
Similarity search - Function
EF-hand domain-containing protein D1/2 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
EF-hand domain-containing protein D1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07380981063 Å
AuthorsMun, S.A. / Park, J. / Park, K.R. / Lee, Y. / Kang, J.Y. / Park, T. / Jin, M. / Yang, J. / Jun, C.D. / Eom, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other private1 Korea, Republic Of
CitationJournal: Front Cell Dev Biol / Year: 2020
Title: Structural and Biochemical Characterization of EFhd1/Swiprosin-2, an Actin-Binding Protein in Mitochondria.
Authors: Mun, S.A. / Park, J. / Park, K.R. / Lee, Y. / Kang, J.Y. / Park, T. / Jin, M. / Yang, J. / Jun, C.D. / Eom, S.H.
History
DepositionJul 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 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: EF-hand domain-containing protein D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4966
Polymers15,1921
Non-polymers3035
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-24 kcal/mol
Surface area6240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.770, 47.556, 87.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein EF-hand domain-containing protein D1 / EF-hand domain-containing protein 1 / Mitocalcin / Swiprosin-2


Mass: 15192.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Efhd1, Sws2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D4J1
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES-NaOH, 5 mM ZnSO4, 25% (v/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 8434 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.1
Reflection shellResolution: 2.07→2.11 Å / Rmerge(I) obs: 0.59 / Num. unique obs: 403

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I2L

5i2l


Resolution: 2.07380981063→43.5995 Å / SU ML: 0.215981547602 / Cross valid method: FREE R-VALUE / σ(F): 1.36030208239 / Phase error: 22.4306799448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228935335343 400 5.06585612969 %
Rwork0.208703349437 7496 -
obs0.209698872726 7896 93.036408625 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.6235678918 Å2
Refinement stepCycle: LAST / Resolution: 2.07380981063→43.5995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 10 23 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074357185132848
X-RAY DIFFRACTIONf_angle_d0.8877657392181130
X-RAY DIFFRACTIONf_chiral_restr0.0480903178683119
X-RAY DIFFRACTIONf_plane_restr0.00564689891253145
X-RAY DIFFRACTIONf_dihedral_angle_d11.7679326915515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.074-2.37390.2607593498931110.2236543779482105X-RAY DIFFRACTION80
2.3739-2.99070.2702330742471340.2275430074822634X-RAY DIFFRACTION99.3895870736
2.9907-43.590.2022472215511550.1963386961632757X-RAY DIFFRACTION99.3517570795

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