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- PDB-1csn: BINARY COMPLEX OF CASEIN KINASE-1 WITH MGATP -

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Basic information

Entry
Database: PDB / ID: 1csn
TitleBINARY COMPLEX OF CASEIN KINASE-1 WITH MGATP
ComponentsCASEIN KINASE-1
KeywordsPHOSPHOTRANSFERASE
Function / homologySerine/threonine-protein kinase, active site / Protein kinase domain profile. / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Protein kinase domain / regulation of 1-phosphatidylinositol-4-phosphate 5-kinase activity / signaling ...Serine/threonine-protein kinase, active site / Protein kinase domain profile. / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Protein kinase domain / regulation of 1-phosphatidylinositol-4-phosphate 5-kinase activity / signaling / fungal-type vacuole / regulation of endocytosis / endocytosis / peptidyl-threonine phosphorylation / protein tyrosine kinase activity / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / plasma membrane / nucleus / cytoplasm / Casein kinase I homolog 1
Function and homology information
Specimen sourceSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2 Å resolution
AuthorsXu, R.-M. / Cheng, X.
Citation
Journal: EMBO J. / Year: 1995
Title: Crystal structure of casein kinase-1, a phosphate-directed protein kinase.
Authors: Xu, R.M. / Carmel, G. / Sweet, R.M. / Kuret, J. / Cheng, X.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Expression, Purification, Crystallization, and Preliminary X-Ray Analysis of Casein Kinase-1 from Schizosaccharomyces Pombe
Authors: Carmel, G. / Leichus, B. / Cheng, X.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 25, 1995 / Release: Jul 31, 1995
RevisionDateData content typeGroupProviderType
1.0Jul 31, 1995Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CASEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1015
Polyers34,3771
Non-polymers7244
Water1,856103
1
A: CASEIN KINASE-1
hetero molecules

A: CASEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,20210
Polyers68,7542
Non-polymers1,4478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
γ
α
β
Length a, b, c (Å)78.960, 78.960, 120.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP 32 2 1

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Components

#1: Protein/peptide CASEIN KINASE-1 /


Mass: 34377.238 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Genus: Schizosaccharomyces
References: UniProt: P40233, Transferases, Transferring phosphorus-containing groups, Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Formula: SO4 / Sulfate
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 / Density percent sol: 60.95 %
Description: THE WAVELENGTH OF 1.0 WAS USED FOR THE NATIVE DATA SETS AND 1.0012 FOR THE HG DERIVATIVE DATA SETS.
Crystal grow
*PLUS
Temp: 16 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Carmel, G., (1994) J.Biol.Chem., 269, 7304.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
10.3 mMprotein1drop
210 mMMOPS1drop
30.1 mMEDTA1drop
40.1 %2-mercaptoethanol1drop
51 mMdithiothreitol1drop
6200 mM1dropNaCl
76 mMATP1drop
81.5 mM1dropMgCl2
91.55 mMammonium sulfate1drop
1050 mMsodium citrate1drop
111.55 mMammonium sulfate1reservoir
1250 mMsodium citrate1reservoir

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Data collection

SourceSource: SYNCHROTRON / Type: NSLS BEAMLINE X12C / Synchrotron site: NSLS / Beamline: X12C / Wavelength: 1.0, 1.0012
DetectorDetector: AREA DETECTOR
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.01.0
21.00121.0
ReflectionNumber obs: 24245 / Rmerge I obs: 0.0804 / Redundancy: 6.7 %
Reflection
*PLUS
D resolution high: 2 / D resolution low: 2 / Number measured all: 161782 / Percent possible obs: 93.9 / Rmerge I obs: 0.0804
Reflection shell
*PLUS
Highest resolution: 2 / Lowest resolution: 2.09 / Percent possible obs: 44.2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
Least-squares processR factor R work: 0.207 / R factor obs: 0.207 / Highest resolution: 2 / Lowest resolution: 11.3 / Number reflection obs: 23860
Refine hist #LASTHighest resolution: 2 / Lowest resolution: 11.3
Number of atoms included #LASTProtein: 2386 / Nucleic acid: 0 / Ligand: 42 / Solvent: 103 / Total: 2531
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Least-squares process
*PLUS
Highest resolution: 2

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