5H0P

Crystal structure of EF-hand protein mutant

> Summary

Summary for 5H0P

DescriptorEF-hand domain-containing protein D2, CALCIUM ION (3 entities in total)
Functional Keywordsef-hand, phosphorylation, metal binding protein
Biological sourceHomo sapiens (Human)
Cellular locationMembrane raft  Q96C19
Total number of polymer chains1
Total molecular weight13831.93
Authors
Park, 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. (deposition date: 2016-10-06, release date: 2017-09-13)
Primary citation
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.
Structural mechanism underlying regulation of human EFhd2/Swiprosin-1 actin-bundling activity by Ser183 phosphorylation.
Biochem. Biophys. Res. Commun., 483:442-448, 2017
PubMed: 28011271 (PDB entries with the same primary citation)
DOI: 10.1016/j.bbrc.2016.12.124
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.862 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.250001.1%2.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5h0p
no rotation
Molmil generated image of 5h0p
rotated about x axis by 90°
Molmil generated image of 5h0p
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AEF-hand domain-containing protein D2polymer12013751.81
UniProt (Q96C19)
Pfam (PF13499)
Homo sapiens (Human)Swiprosin-1
CALCIUM IONnon-polymer40.12
waterwater18.039

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight13751.8
Non-Polymers*Number of molecules2
Total molecular weight80.2
All*Total molecular weight13831.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.862 Å)

Cell axes36.67551.10553.650
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits29.80 - 1.86
the highest resolution shell value1.979 - 1.862
R-factor0.2009
R-work0.19600
the highest resolution shell value0.218
R-free0.24630
the highest resolution shell value0.311
RMSD bond length0.008
RMSD bond angle1.013

Data Collection Statistics

Resolution limits50.00 - 1.86
the highest resolution shell value -
Number of reflections8596
the highest resolution shell value0.315
Completeness96.9
Redundancy13.2
the highest resolution shell value13.2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP8.5290

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16binding site for residue CA A 201
ChainResidue
AASP105
AASP109
APHE111
AGLU116
AHOH303
AHOH337

AC26binding site for residue CA A 202
ChainResidue
AASP141
AASP143
AASP145
ALYS147
AGLU152
AHOH320

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI1122. {ECO:0000255|PROSITE- ProRule:PRU00448}
ChainResidueDetails
AASP77-GLU88

SWS_FT_FI2121. {ECO:0000255|PROSITE- ProRule:PRU00448}
ChainResidueDetails
AASP41-GLU52

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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