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- PDB-1iq5: Calmodulin/nematode CA2+/Calmodulin dependent kinase kinase fragment -

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Basic information

Entry
Database: PDB / ID: 1iq5
TitleCalmodulin/nematode CA2+/Calmodulin dependent kinase kinase fragment
Components
  • CA2+/CALMODULIN DEPENDENT KINASE KINASE
  • CALMODULIN
KeywordsMETAL BINDING PROTEIN/PROTEIN BINDING / EF-hand / CALMODULIN / PROTEIN-PEPTIDE COMPLEX / METAL BINDING PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of RAC1 downstream of NMDARs / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/calmodulin-dependent protein kinase activity / myosin II complex / calcium-mediated signaling / calmodulin binding / signaling receptor binding ...CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of RAC1 downstream of NMDARs / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/calmodulin-dependent protein kinase activity / myosin II complex / calcium-mediated signaling / calmodulin binding / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 B / Calcium/calmodulin-dependent protein kinase kinase / :
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKurokawa, H. / Osawa, M. / Kurihara, H. / Katayama, N. / Tokumitsu, H. / Swindells, M.B. / Kainosho, M. / Ikura, M.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca(2+)/calmodulin-dependent kinase kinase peptide
Authors: Kurokawa, H. / Osawa, M. / Kurihara, H. / Katayama, N. / Tokumitsu, H. / Swindells, M.B. / Kainosho, M. / Ikura, M.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase
Authors: Osawa, M. / Tokumitsu, H. / Swindells, M.B. / Kurihara, H. / Orita, M. / Shibanuma, T. / Furuya, T. / Ikura, M.
History
DepositionJun 14, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: CALMODULIN
B: CA2+/CALMODULIN DEPENDENT KINASE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2126
Polymers20,0512
Non-polymers1604
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-77 kcal/mol
Surface area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.090, 84.400, 59.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CALMODULIN


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PAS / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS
#2: Protein/peptide CA2+/CALMODULIN DEPENDENT KINASE KINASE


Mass: 3198.920 Da / Num. of mol.: 1 / Fragment: CALMODULIN BINDING DOMAIN (RESIDUES 331-357) / Source method: obtained synthetically
Details: This sequence occurs naturally in Caenorhabditis elegans
References: UniProt: Q8T8D4, UniProt: Q3Y416*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, citratet, sodium tartrae, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mcitrate-NaOH1reservoir
22.0 Mammonium sulfate1reservoir
30.2 Msodium tartrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: IMAGE PLATE / Date: Feb 10, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 57477 / Num. obs: 17155 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 25.798 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 21.9
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.212 / % possible all: 89.1
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 57477
Reflection shell
*PLUS
% possible obs: 89.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→100 Å / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1695 9.9688 %RANDOM
Rwork0.217 ---
all-17155 --
obs-17003 --
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 4 67 1396
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 100 Å / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.134
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.612
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.631
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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