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- PDB-1kwa: HUMAN CASK/LIN-2 PDZ DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1kwa
TitleHUMAN CASK/LIN-2 PDZ DOMAIN
ComponentsHCASK/LIN-2 PROTEIN
KeywordsKINASE / PDZ DOMAIN / NEUREXIN / SYNDECAN / RECEPTOR CLUSTERING
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / neurexin family protein binding / negative regulation of wound healing / regulation of neurotransmitter secretion / Dopamine Neurotransmitter Release Cycle / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Nephrin family interactions ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / neurexin family protein binding / negative regulation of wound healing / regulation of neurotransmitter secretion / Dopamine Neurotransmitter Release Cycle / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / 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 / Syndecan interactions / positive regulation of calcium ion import / basement membrane / negative regulation of cell-matrix adhesion / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / protein localization / presynaptic membrane / basolateral plasma membrane / vesicle / histone H2AS1 kinase activity / cell adhesion / calmodulin binding / non-specific serine/threonine protein kinase / signaling receptor binding / protein serine/threonine kinase activity / protein serine kinase activity / focal adhesion / protein phosphorylation / 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 / Pdz3 Domain / 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 / Roll / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, SIR / Resolution: 1.93 Å
AuthorsDaniels, D.L. / Cohen, A.R. / Anderson, J.M. / Brunger, A.T.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition
Authors: Daniels, D.L. / Cohen, A.R. / Anderson, J.M. / Brunger, A.T.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal Structures of a Complexed and Peptide-Free Membrane Protein-Binding Domain: Molecular Basis of Peptide Recognition by Pdz
Authors: Doyle, D.A. / Lee, A. / Lewis, J. / Kim, E. / Sheng, M. / Mackinnon, R.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HCASK/LIN-2 PROTEIN
B: HCASK/LIN-2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6785
Polymers20,3902
Non-polymers2883
Water3,333185
1
A: HCASK/LIN-2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3873
Polymers10,1951
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HCASK/LIN-2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2912
Polymers10,1951
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: HCASK/LIN-2 PROTEIN
B: HCASK/LIN-2 PROTEIN
hetero molecules

A: HCASK/LIN-2 PROTEIN
B: HCASK/LIN-2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,35610
Polymers40,7794
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
Buried area6080 Å2
ΔGint-126 kcal/mol
Surface area17120 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-54 kcal/mol
Surface area9640 Å2
MethodPISA
5
A: HCASK/LIN-2 PROTEIN
hetero molecules

B: HCASK/LIN-2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6785
Polymers20,3902
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
Buried area1470 Å2
ΔGint-40 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.800, 97.000, 92.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

21B-3-

HOH

31B-85-

HOH

41B-100-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.417572, 0.546936, 0.7256), (-0.782662, -0.189174, 0.593004), (0.461599, -0.815521, 0.349072)
Vector: -71.2218, 92.4814, 109.0678)

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Components

#1: Protein HCASK/LIN-2 PROTEIN / HCASK / GLGF REPEAT / DHR


Mass: 10194.873 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CLONED FROM A CDNA LIVER LIBRARY / Cellular location: MEMBRANE-ASSOCIATED / Gene: HCASK / Organ: LIVER / Plasmid: N-TERMINAL GST FUSION, AMP RESISTANT / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: O14936
#2: Chemical ChemComp-SO4 / SULFATE ION / HCASK / GLGF REPEAT / DHR


Mass: 96.063 Da / Num. of mol.: 3 / Fragment: PDZ DOMAIN / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.3 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 294 K / pH: 6.5
Details: PROTEIN WAS CRYSTALLIZED IN 1.8M AMMONIUM SULFATE AND 100MM MES PH 6.5 AT 21 DEGREES C., temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlhCASK1drop
20.9 Mammonium sulfate1drop
350 mMMES1drop
41.8 Mammonium sulfate1reservoir
5100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979 / Wavelength: 0.979, 1.033
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Dec 1, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.0331
ReflectionResolution: 1.93→30 Å / Num. obs: 14216 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 13 Å2 / Rsym value: 0.032 / Net I/σ(I): 21.6
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.293 / % possible all: 78.1
Reflection
*PLUS
Num. measured all: 50697 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 78.1 % / Rmerge(I) obs: 0.293

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Processing

RefinementMethod to determine structure: MAD, SIR / Resolution: 1.93→30 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1278 9.4 %RANDOM
Rwork0.251 ---
obs0.251 13564 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.61 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å20 Å2
2--0.52 Å20 Å2
3---3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.93→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 15 185 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 204 9.4 %
Rwork0.278 1957 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SULPHATE_ION.PARA
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor obs: 0.278

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