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- PDB-5h0p: Crystal structure of EF-hand protein mutant -

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Basic information

Entry
Database: PDB / ID: 5h0p
TitleCrystal structure of EF-hand protein mutant
ComponentsEF-hand domain-containing protein D2
KeywordsMETAL BINDING PROTEIN / EF-hand / Phosphorylation
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 / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF-hand domain-containing protein D1/2 / : / Allograft inflammatory factor 1 / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EF-hand domain-containing protein D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.862 Å
AuthorsPark, K.R. / An, J.Y. / Kang, J.Y. / Lee, J.G. / Youn, H.S. / Lee, Y. / Mun, S.A. / Jun, C.D. / Song, W.K. / Eom, S.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural mechanism underlying regulation of human EFhd2/Swiprosin-1 actin-bundling activity by Ser183 phosphorylation.
Authors: Park, K.R. / An, J.Y. / Kang, J.Y. / Lee, J.G. / Lee, Y. / Mun, S.A. / Jun, C.D. / Song, W.K. / Eom, S.H.
History
DepositionOct 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8323
Polymers13,7521
Non-polymers802
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.675, 51.105, 53.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13751.778 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-184 / Mutation: S183E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFHD2, SWS1 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96C19
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.83 Å3/Da / Density % sol: 32.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M trimethlyamine-N-oxide dihydrate, 0.1 M Tris-HCl (pH 8.5), 20% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9897 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9897 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 8596 / % possible obs: 96.9 % / Redundancy: 13.2 % / Net I/σ(I): 22.7
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 6.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I2L

5i2l


Resolution: 1.862→29.796 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 27.37
RfactorNum. reflection% reflection
Rfree0.2463 873 10.16 %
Rwork0.196 --
obs0.2009 8596 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.862→29.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 2 39 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008842
X-RAY DIFFRACTIONf_angle_d1.0131120
X-RAY DIFFRACTIONf_dihedral_angle_d12.984332
X-RAY DIFFRACTIONf_chiral_restr0.078119
X-RAY DIFFRACTIONf_plane_restr0.004145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8624-1.97910.31141450.2181270X-RAY DIFFRACTION98
1.9791-2.13180.27611460.19731296X-RAY DIFFRACTION99
2.1318-2.34630.26711400.19041294X-RAY DIFFRACTION99
2.3463-2.68560.26941510.18941318X-RAY DIFFRACTION100
2.6856-3.38280.26061520.20141318X-RAY DIFFRACTION99
3.3828-29.80010.21331390.19381227X-RAY DIFFRACTION87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.27082.1146-3.7538.1594-2.71792.867-0.04570.1562-0.4393-0.1797-0.03770.26130.3855-0.50710.03430.276-0.0697-0.01760.2599-0.02680.3005-20.8945-7.47113.996
29.27860.0674-2.41932.9290.77736.13480.01990.75170.3366-0.52730.142-0.159-0.4211-0.1047-0.10090.3691-0.0430.00870.21360.04190.2019-12.51473.7644-3.6215
36.61461.72912.48167.98862.688.22460.1489-0.2017-0.71460.3712-0.0435-0.77610.13510.2737-0.18570.2204-0.0594-0.03510.20520.08290.2916-12.9423-4.92035.8227
47.9056-2.23453.11048.9856-2.0894.95070.2125-0.88860.08150.2912-0.06570.0372-0.2758-0.1318-0.14890.2803-0.01710.07190.2181-0.03240.1804-14.14585.48229.6663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 182 )

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