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- PDB-4cln: STRUCTURE OF A RECOMBINANT CALMODULIN FROM DROSOPHILA MELANOGASTE... -

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Basic information

Entry
Database: PDB / ID: 4cln
TitleSTRUCTURE OF A RECOMBINANT CALMODULIN FROM DROSOPHILA MELANOGASTER REFINED AT 2.2-ANGSTROMS RESOLUTION
ComponentsCALMODULIN
KeywordsCALCIUM BINDING PROTEIN
Function / homology
Function and homology information


metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development / myosin V complex / : ...metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development / myosin V complex / : / kinetochore organization / : / actin filament-based movement / rhodopsin mediated signaling pathway / Neutrophil degranulation / myosin V binding / channel regulator activity / cellular response to ethanol / muscle cell cellular homeostasis / myosin heavy chain binding / mitotic spindle pole / centriole replication / enzyme regulator activity / centriole / sensory perception of sound / spindle / mitotic spindle / sensory perception of smell / cell cortex / midbody / protein phosphorylation / centrosome / calcium ion binding / nucleoplasm / cytosol / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsTaylor, D.A. / Sack, J.S. / Maune, J.F. / Beckingham, K. / Quiocho, F.A.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-A resolution.
Authors: Taylor, D.A. / Sack, J.S. / Maune, J.F. / Beckingham, K. / Quiocho, F.A.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Structure and Sequence of the Drosophila Melanogaster Calmodulin Gene
Authors: Smith, V.L. / Doyle, K.E. / Maune, J.F. / Munjaal, R.P. / Beckingham, K.
History
DepositionJun 24, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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 / 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_database_status.process_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8555
Polymers16,6941
Non-polymers1604
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.570, 53.920, 24.780
Angle α, β, γ (deg.)93.24, 97.08, 88.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CALMODULIN /


Mass: 16694.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P62152
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / pH: 4 / Details: initial seeding crystal
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %(v/v)MPD1reservoir
215 %(v/v)ethanol1reservior
35 mMcalcium chloride1reservoir
420 mMsodium acetate1reservoir
55.3 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 6831 / % possible obs: 81.7 % / Observed criterion σ(F): 2 / Num. measured all: 10617 / Rmerge F obs: 0.068

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.197 5239
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 4 78 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0430.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0670.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4652
X-RAY DIFFRACTIONp_mcangle_it2.243
X-RAY DIFFRACTIONp_scbond_it1.4442
X-RAY DIFFRACTIONp_scangle_it2.1853
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.2240.15
X-RAY DIFFRACTIONp_singtor_nbd0.2560.5
X-RAY DIFFRACTIONp_multtor_nbd0.4280.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.370.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.73
X-RAY DIFFRACTIONp_staggered_tor26.315
X-RAY DIFFRACTIONp_orthonormal_tor31.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: 'X-PLOR, PROLSQ' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. reflection obs: 5239 / σ(F): 2 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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