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- PDB-5i2l: Structure of EF-hand containing protein -

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Basic information

Entry
Database: PDB / ID: 5i2l
TitleStructure of EF-hand containing protein
ComponentsEF-hand domain-containing protein D2
KeywordsMETAL BINDING PROTEIN / Calcium binding protein
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 / MAD / Resolution: 1.85 Å
AuthorsPark, K.R. / Kwon, M.S. / An, J.Y. / Lee, J.G. / Youn, H.S. / Lee, Y. / Kang, J.Y. / Kim, T.G. / Lim, J.J. / Park, J.S. ...Park, K.R. / Kwon, M.S. / An, J.Y. / Lee, J.G. / Youn, H.S. / Lee, Y. / Kang, J.Y. / Kim, T.G. / Lim, J.J. / Park, J.S. / Lee, S.H. / Song, W.K. / Cheong, H. / Jun, C. / Eom, S.H.
CitationJournal: Sci Rep / Year: 2016
Title: Structural implications of Ca(2+)-dependent actin-bundling function of human EFhd2/Swiprosin-1.
Authors: Park, K.R. / Kwon, M.S. / An, J.Y. / Lee, J.G. / Youn, H.S. / Lee, Y. / Kang, J.Y. / Kim, T.G. / Lim, J.J. / Park, J.S. / Lee, S.H. / Song, W.K. / Cheong, H.K. / Jun, C.D. / Eom, S.H.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: EF-hand domain-containing protein D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7903
Polymers13,7101
Non-polymers802
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-25 kcal/mol
Surface area6190 Å2
Unit cell
Length a, b, c (Å)37.325, 50.670, 53.381
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: 13709.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFHD2, SWS1 / Plasmid: 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.: 114 / 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: 1.99 Å3/Da / Density % sol: 33.19 % / Description: Rod shape
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 23% PEG 4000, 0.16M Na-acetate, 3% dioxane, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796, 0.9793, 0.9716, 0.9873,1.0000
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97931
30.97161
40.98731
511
ReflectionResolution: 1.85→50 Å / Num. obs: 8999 / % possible obs: 99.3 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 9.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-2000data collection
HKL-2000data processing
PHENIX1.7.2_869phasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→36.75 Å / SU ML: 0.41 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.66
RfactorNum. reflection% reflection
Rfree0.2068 432 4.79 %
Rwork0.162 --
obs0.1667 8598 99.22 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 41.781 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8923 Å20 Å2-0 Å2
2---1.0162 Å20 Å2
3----4.8762 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms854 0 2 114 970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008870
X-RAY DIFFRACTIONf_angle_d1.151159
X-RAY DIFFRACTIONf_dihedral_angle_d15.034339
X-RAY DIFFRACTIONf_chiral_restr0.09124
X-RAY DIFFRACTIONf_plane_restr0.004150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8489-2.11640.20721390.16772778X-RAY DIFFRACTION98
2.1164-2.66640.23061460.16192843X-RAY DIFFRACTION99
2.6664-36.75740.1951470.16512975X-RAY DIFFRACTION100
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)
10.1790.0531-0.16880.0331-0.03520.35490.0122-0.27340.07770.03920.3881-0.54050.02680.25480.01410.20310.0699-0.02580.1628-0.01580.3529-15.8816.1109-6.3151
20.30490.02240.22060.8203-0.04830.4167-0.0542-0.04280.102-0.02120.01790.23780.0233-0.2418-0.08560.05360.0247-0.01230.08990.02140.1058-21.51726.3236-2.7948
30.1054-0.04240.09410.20320.02530.4001-0.0566-0.2764-0.10920.32120.1545-0.09850.5036-0.6180.07990.159-0.0385-0.0020.09020.03850.1416-18.8083-8.02293.5764
40.06690.13070.04710.4532-0.00740.0037-0.1984-0.1616-0.2724-0.31360.1315-0.36180.27650.21160.00710.12330.0173-0.01050.11280.01940.1565-8.0398-4.88152.9365
50.0372-0.02720.02780.7404-0.03430.00320.01790.0510.07270.2088-0.04740.2702-0.35330.27670.00050.1255-0.0331-0.03520.152500.0704-8.33125.80194.8283
60.4536-0.12390.05170.0262-0.02970.41770.08420.07290.0294-0.0448-0.0133-0.1508-0.044-0.02770.03830.103-0.0035-0.00080.1162-0.00230.1008-11.31561.0769-7.5954
70.2655-0.10.01310.08180.04160.3415-0.03820.2779-0.1795-0.47390.16430.24630.10290.12850.03750.2191-0.0376-0.04620.1242-0.00170.1506-18.2973-3.9052-10.5574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 80:85)
2X-RAY DIFFRACTION2chain 'A' and (resseq 86:113)
3X-RAY DIFFRACTION3chain 'A' and (resseq 114:129)
4X-RAY DIFFRACTION4chain 'A' and (resseq 130:140)
5X-RAY DIFFRACTION5chain 'A' and (resseq 141:149)
6X-RAY DIFFRACTION6chain 'A' and (resseq 150:169)
7X-RAY DIFFRACTION7chain 'A' and (resseq 170:184)

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