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- PDB-7ygv: Crystal structure of the Ca2+-bound EFhd1/Swiprosin-2 -

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Basic information

Entry
Database: PDB / ID: 7ygv
TitleCrystal structure of the Ca2+-bound EFhd1/Swiprosin-2
ComponentsEF-hand domain-containing protein D1
KeywordsMETAL BINDING PROTEIN / mitochondria / EF-hand containing protein
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: 2.8 Å
AuthorsMun, S.A. / Park, J. / Kang, J.Y. / Park, T. / Jin, M. / Ynag, J. / Eom, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1A2C1006267 Korea, Republic Of
Other private
CitationJournal: Iucrj / Year: 2023
Title: Structural and biochemical insights into Zn 2+ -bound EF-hand proteins, EFhd1 and EFhd2.
Authors: Mun, S.A. / Park, J. / Kang, J.Y. / Park, T. / Jin, M. / Yang, J. / Eom, S.H.
History
DepositionJul 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)14,8305
Polymers14,5931
Non-polymers2384
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-19 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.251, 47.907, 63.434
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: 14592.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: [GAMGS + EFhd1(69-193)](GAMGS: the cleaved site after GST-TEV tag cleavage)
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.4 mM ZnSO4, and 25% (w/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: 1.28255 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28255 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 3596 / % possible obs: 99.8 % / Redundancy: 22 % / Biso Wilson estimate: 45.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 20
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 176 / CC1/2: 0.959 / Rpim(I) all: 0.15 / Rrim(I) all: 0.517

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1-4487phasing
Coot0.8.6.1model building
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CLT

7clt


Resolution: 2.8→31.72 Å / SU ML: 0.3108 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 600 9.88 %
Rwork0.1947 5472 -
obs0.2004 6072 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 9 20 856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093848
X-RAY DIFFRACTIONf_angle_d1.03891130
X-RAY DIFFRACTIONf_chiral_restr0.0562119
X-RAY DIFFRACTIONf_plane_restr0.0058145
X-RAY DIFFRACTIONf_dihedral_angle_d17.4408325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.23231230.24351231X-RAY DIFFRACTION84.47
3.08-3.530.31221570.20161439X-RAY DIFFRACTION99.5
3.53-4.440.22911580.18641443X-RAY DIFFRACTION99.94
4.45-31.720.25181620.18321359X-RAY DIFFRACTION94.47

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