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- PDB-3mft: CASK-4M CaM Kinase Domain, Mn2+ -

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Basic information

Entry
Database: PDB / ID: 3mft
TitleCASK-4M CaM Kinase Domain, Mn2+
ComponentsPeripheral plasma membrane protein CASK
KeywordsTRANSFERASE / Catalytic mechanism / kinase catalysis / Mg2+-mediated phosphate transfer / protein kinase
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / Assembly and cell surface presentation of NMDA receptors / calcium ion import / Nephrin family interactions ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / Assembly and cell surface presentation of NMDA receptors / calcium ion import / Nephrin family interactions / Sensory processing of sound by outer hair cells of the cochlea / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / ciliary membrane / regulation of synaptic vesicle exocytosis / negative regulation of cell-matrix adhesion / Syndecan interactions / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / protein localization / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / signaling receptor binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWahl, M.C. / Mukherjee, K.
CitationJournal: Sci.Signal. / Year: 2010
Title: Evolution of CASK into a Mg2+-sensitive kinase.
Authors: Mukherjee, K. / Sharma, M. / Jahn, R. / Wahl, M.C. / Sudhof, T.C.
History
DepositionApr 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)39,2911
Polymers39,2911
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.943, 61.811, 101.463
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 Peripheral plasma membrane protein CASK / hCASK / Calcium/calmodulin-dependent serine protein kinase / Protein lin-2 homolog


Mass: 39291.047 Da / Num. of mol.: 1 / Fragment: CASK-4M CaM kinase domain, residues 1-337 / Mutation: Pro22Ala, His145Glu, Gly162Asp, Cys146Asn
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 12.5 % (v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.87856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.87856 Å / Relative weight: 1
ReflectionResolution: 2.2→42.66 Å / Num. all: 36351 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1513 / Rsym value: 0.568 / % possible all: 84.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C0I

3c0i


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.035 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.276 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26997 969 5.1 %RANDOM
Rwork0.21048 ---
all0.21352 18431 --
obs0.21352 17889 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---2.92 Å20 Å2
3---2.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 0 138 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222477
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9673342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98323.009113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96415447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6821520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021864
X-RAY DIFFRACTIONr_nbd_refined0.1990.21111
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.28
X-RAY DIFFRACTIONr_mcbond_it0.5491.51553
X-RAY DIFFRACTIONr_mcangle_it0.94222429
X-RAY DIFFRACTIONr_scbond_it1.31631046
X-RAY DIFFRACTIONr_scangle_it2.114.5913
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 60 -
Rwork0.285 1120 -
obs-1180 84.23 %
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)
14.586-3.92220.60016.08-0.00060.5235-0.0645-0.4251-0.07480.8010.16410.3699-0.06-0.0198-0.09950.079-0.0370.086-0.0993-0.056-0.0154-33.75215.3613.936
20.6577-0.01840.11351.79760.03332.38310.0626-0.0256-0.06860.0144-0.04280.12180.2447-0.0766-0.0199-0.0148-0.0267-0.0074-0.1357-0.00510.0214-26.683-5.014-11.227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 94
2X-RAY DIFFRACTION2A95 - 306

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