5DSU

Crystal structure of double mutant of N-domain of human calmodulin

> Summary

Summary for 5DSU

DescriptorCalmodulin, CALCIUM ION, TRIETHYLENE GLYCOL, ... (4 entities in total)
Functional Keywordsca2+ binding protein ef-hand domain, signaling protein
Biological sourceHomo sapiens (Human)
Cellular locationCytoplasm, cytoskeleton, spindle  P62158
Total number of polymer chains1
Total molecular weight9022.16
Authors
Ababou, A.,Zaleska, M. (deposition date: 2015-09-17, release date: 2017-01-11, Last modification date: 2017-04-12)
Primary citation
Ababou, A.,Zaleska, M.,Pfuhl, M.
On the Ca(2+) binding and conformational change in EF-hand domains: Experimental evidence of Ca(2+)-saturated intermediates of N-domain of calmodulin.
Biochim. Biophys. Acta, 1865:640-651, 2017
PubMed: 28288938 (PDB entries with the same primary citation)
DOI: 10.1016/j.bbapap.2017.03.003
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.93 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2683010.9%2.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ACalmodulinpolymer788791.81
UniProt (P62158)
UniProt (by SIFTS) (P0DP24)
Homo sapiens (Human)CaM
CALCIUM IONnon-polymer40.12
TRIETHYLENE GLYCOLnon-polymer150.21
waterwater18.056

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight8791.8
Non-Polymers*Number of molecules3
Total molecular weight230.3
All*Total molecular weight9022.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.93 Å)

Cell axes38.40038.40081.200
Cell angles90.0090.00120.00
SpacegroupP 32 2 1
Resolution limits20.99 - 1.93
the highest resolution shell value2.431 - 1.930
R-factor0.2303
R-work0.22850
the highest resolution shell value0.262
R-free0.26410
the highest resolution shell value0.348
RMSD bond length0.012
RMSD bond angle1.312

Data Collection Statistics

Resolution limits20.99 - 1.93
the highest resolution shell value -
Number of reflections5544
Completeness99.0
Redundancy4.7
the highest resolution shell value3.6

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7.5290

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
A0005737cellular_componentcytoplasm
A0000922cellular_componentspindle pole
A0019855molecular_functioncalcium channel inhibitor activity
A0005509molecular_functioncalcium ion binding
A0060315biological_processnegative regulation of ryanodine-sensitive calcium-release channel activity
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16binding site for residue CA A 101
ChainResidue
AASP20
AASP22
AASP24
ATHR26
AGLU31
AHOH211

AC26binding site for residue CA A 102
ChainResidue
AASP56
AASP58
AASN60
ATHR62
AGLU67
AHOH237

AC34binding site for residue PGE A 103
ChainResidue
ATYR19
ALEU39
AMET72
AILE75

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

site_idNumber of ResiduesDetails
PGE_5dsu_A_1037TRIETHYLENE GLYCOL binding site
ChainResidueligand
AALA15PGE: TRIETHYLENE GLYCOL
ALEU18-TYR19PGE: TRIETHYLENE GLYCOL
AVAL35-MET36PGE: TRIETHYLENE GLYCOL
ALEU39PGE: TRIETHYLENE GLYCOL
AMET72PGE: TRIETHYLENE GLYCOL

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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
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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