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- PDB-7ygy: Crystal structure of the Zn2+-bound EFhd2/Swiprosin-1 -

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Basic information

Entry
Database: PDB / ID: 7ygy
TitleCrystal structure of the Zn2+-bound EFhd2/Swiprosin-1
ComponentsEF-hand domain-containing protein D2
KeywordsMETAL BINDING PROTEIN / EF-hand containing protein / cytosol
Function / homology
Function and homology information


RHOD GTPase cycle / cadherin binding / membrane raft / calcium ion binding
Similarity search - Function
EF-hand domain-containing protein D1/2 / : / Allograft inflammatory factor 1 / 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 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMun, S.A. / Park, J. / Kang, J.Y. / Park, T. / Jin, M. / Yang, J. / Eom, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1A2C1006267 Korea, Republic Of
Other privateGIST Research Institute (GRI) IIBR Korea, Republic Of
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 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9064
Polymers13,7101
Non-polymers1963
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-18 kcal/mol
Surface area5830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.900, 92.900, 92.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein EF-hand domain-containing protein D2 / Swiprosin-1


Mass: 13709.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-184
Source method: isolated from a genetically manipulated source
Details: [GAMGS + EFhd2(70-184)] - GAMGS: the cleaved site after GST-TEV tag cleavage - GEPQSPSRRVFN: Part of PR domain in EFhd2, disordered - DVSS: disordered
Source: (gene. exp.) Homo sapiens (human) / Gene: EFHD2, SWS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96C19
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES-NaOH pH 7.5, 25% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2851 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2851 Å / Relative weight: 1
ReflectionResolution: 2.6→65.67 Å / Num. obs: 4243 / % possible obs: 100 % / Redundancy: 80.8 % / Biso Wilson estimate: 71.7 Å2 / CC1/2: 1 / Net I/σ(I): 40.3
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 518 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
PHENIX1.20.1-4487phasing
Coot0.8.6.1model building
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I2L

5i2l


Resolution: 2.6→46.45 Å / SU ML: 0.2248 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.6291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2595 209 4.94 %
Rwork0.2288 4026 -
obs0.2304 4235 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 3 5 783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0104787
X-RAY DIFFRACTIONf_angle_d1.18421053
X-RAY DIFFRACTIONf_chiral_restr0.058115
X-RAY DIFFRACTIONf_plane_restr0.0086137
X-RAY DIFFRACTIONf_dihedral_angle_d18.7644294
LS refinement shellResolution: 2.6→46.45 Å
RfactorNum. reflection% reflection
Rfree0.2595 209 -
Rwork0.2288 4026 -
obs--99.83 %

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