5DSU

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

> Summary

Summary for 5DSU

DescriptorCalmodulin
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)
Primary citation
Ababou, A.,Zaleska, M.
Crystal structure of double mutant of N-domain of human calmodulin
To Be Published,
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)
Pfam (PF13499)
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
A0005813cellular_componentcentrosome
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0070062cellular_componentextracellular exosome
A0005576cellular_componentextracellular region
A0030426cellular_componentgrowth cone
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0005886cellular_componentplasma membrane
A0014069cellular_componentpostsynaptic density
A0030017cellular_componentsarcomere
A0005876cellular_componentspindle microtubule
A0000922cellular_componentspindle pole
A0031982cellular_componentvesicle
A0008076cellular_componentvoltage-gated potassium channel complex
A0005509molecular_functioncalcium ion binding
A0008440molecular_functioninositol-1,4,5-trisphosphate 3-kinase activity
A0044325molecular_functionion channel binding
A0015276molecular_functionligand-gated ion channel activity
A0031997molecular_functionN-terminal myristoylation domain binding
A0030235molecular_functionnitric-oxide synthase regulator activity
A0043274molecular_functionphospholipase binding
A0019904molecular_functionprotein domain specific binding
A0019901molecular_functionprotein kinase binding
A0072542molecular_functionprotein phosphatase activator activity
A0043539molecular_functionprotein serine/threonine kinase activator activity
A0005088molecular_functionRas guanyl-nucleotide exchange factor activity
A0031996molecular_functionthioesterase binding
A0031432molecular_functiontitin binding
A0007190biological_processactivation of adenylate cyclase activity
A0005513biological_processdetection of calcium ion
A0038095biological_processFc-epsilon receptor signaling pathway
A0007186biological_processG-protein coupled receptor signaling pathway
A0000086biological_processG2/M transition of mitotic cell cycle
A0005980biological_processglycogen catabolic process
A0043647biological_processinositol phosphate metabolic process
A0000165biological_processMAPK cascade
A0006936biological_processmuscle contraction
A0010801biological_processnegative regulation of peptidyl-threonine phosphorylation
A0060315biological_processnegative regulation of ryanodine-sensitive calcium-release channel activity
A0002576biological_processplatelet degranulation
A0030801biological_processpositive regulation of cyclic nucleotide metabolic process
A0051343biological_processpositive regulation of cyclic-nucleotide phosphodiesterase activity
A0043388biological_processpositive regulation of DNA binding
A0051000biological_processpositive regulation of nitric-oxide synthase activity
A0010800biological_processpositive regulation of peptidyl-threonine phosphorylation
A0032516biological_processpositive regulation of phosphoprotein phosphatase activity
A0031954biological_processpositive regulation of protein autophosphorylation
A0035307biological_processpositive regulation of protein dephosphorylation
A0071902biological_processpositive regulation of protein serine/threonine kinase activity
A0060316biological_processpositive regulation of ryanodine-sensitive calcium-release channel activity
A0006479biological_processprotein methylation
A0055117biological_processregulation of cardiac muscle contraction
A0010881biological_processregulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
A1901844biological_processregulation of cell communication by electrical coupling involved in cardiac conduction
A0032465biological_processregulation of cytokinesis
A0002027biological_processregulation of heart rate
A1901841biological_processregulation of high voltage-gated calcium channel activity
A0050999biological_processregulation of nitric-oxide synthase activity
A0010880biological_processregulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
A0022400biological_processregulation of rhodopsin mediated signaling pathway
A0001975biological_processresponse to amphetamine
A0051592biological_processresponse to calcium ion
A0051412biological_processresponse to corticosterone
A0021762biological_processsubstantia nigra development
A0007223biological_processWnt signaling pathway, calcium modulating pathway
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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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