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- PDB-1deg: THE LINKER OF DES-GLU84 CALMODULIN IS BENT AS SEEN IN THE CRYSTAL... -

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Entry
Database: PDB / ID: 1deg
TitleTHE LINKER OF DES-GLU84 CALMODULIN IS BENT AS SEEN IN THE CRYSTAL STRUCTURE
ComponentsCALMODULIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / positive regulation of DNA binding / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / spindle pole / response to calcium ion / calcium-dependent protein binding / disordered domain specific binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / vesicle / transmembrane transporter binding / protein autophosphorylation / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsRaghunathan, S. / Chandross, R. / Cheng, B.P. / Persechini, A. / Sobottk, S.E. / Kretsinger, R.H.
Citation
#1: Journal: Biochemistry / Year: 1991
Title: Small-Angle X-Ray Scattering Studies of Calmodulin Mutants with Deletions in the Linker Region of the Central Helix Indicate that the Linker Region Retains a Predominantly A-Helical Conformation
Authors: Kataoka, M. / Head, J.F. / Persechini, A. / Kretsinger, R.H. / Engelman, D.M.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Calmodulins with Deletions in the Central Helix Functionally Replace the Native Protein in Yeast Cells
Authors: Persechini, A. / Kretsinger, R.H. / Davis, T.N.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: The Effects of Deletions in the Central Helix of Calmodulin on Enzyme Activation and Peptide Binding
Authors: Persechini, A. / Blumenthal, D.K. / Jarrett, H.W. / Klee, C.B. / Hardy, D.O. / Kretsinger, R.H.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: The Central Helix of Calmodulin Functions as a Flexible Tether
Authors: Persechini, A. / Kretsinger, R.H.
#5: Journal: J.CARDIOVASC.PHARMACOL. / Year: 1988
Title: Toward a Model of the Calmodulin-Myosin Light Chain Kinase Complex: Implications of Calmodulin Function
Authors: Persechini, A. / Kretsinger, R.H.
History
DepositionJun 7, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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
Remark 650HELIX THERE IS A BEND OF 40 DEGREES BETWEEN THE F2 HELIX RESIDUES 66 - 76, AND THE LINKER 77 - 83. ...HELIX THERE IS A BEND OF 40 DEGREES BETWEEN THE F2 HELIX RESIDUES 66 - 76, AND THE LINKER 77 - 83. THE ANGLE BETWEEN THE LINKER AND THE E3 HELIX, 85 - 92, IS 85 DEGREES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1955
Polymers16,0351
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.300, 49.900, 62.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.990874, 0.076905, 0.110695), (0.098889, 0.972835, 0.209316), (-0.09159, 0.218352, -0.971562)
Vector: 109.81735, -8.59274, -30.20036)
DetailsTHERE IS AN APPROXIMATE NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS ROUGHLY PARALLEL TO B, RELATING DOMAIN I, (RESIDUES 12 - 74) AND DOMAIN II (RESIDUES 85 - 147). THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR DOMAIN I WHEN APPLIED TO DOMAIN II.

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Components

#1: Protein CALMODULIN / / Coordinate model: Cα atoms only


Mass: 16034.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: BRAIN / Plasmid: CLASSIFIED / References: UniProt: P02593, UniProt: P62157*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: CALM_HUMAN SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 129 ASN 129

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.1 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %satammonium sulfate1reservoir
210 mM1reservoirCaCl2
350 mMMES1reservoir
410 mg/mlprotein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. all: 3483 / Num. obs: 3396 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3.1 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.23 / Rfactor obs: 0.23 / Highest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms142 0 4 0 146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
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_deg5.49
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

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