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- PDB-1a29: CALMODULIN COMPLEXED WITH TRIFLUOPERAZINE (1:2 COMPLEX) -

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Basic information

Entry
Database: PDB / ID: 1a29
TitleCALMODULIN COMPLEXED WITH TRIFLUOPERAZINE (1:2 COMPLEX)
ComponentsCALMODULIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / spindle pole / protein domain specific binding / calcium ion binding / protein-containing complex / 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
Chem-TFP / Calmodulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsBocskei, Zs. / Harmat, V. / Vertessy, B.G. / Ovadi, J. / Naray-Szabo, G.
Citation
Journal: Biochemistry / Year: 1998
Title: Simultaneous binding of drugs with different chemical structures to Ca2+-calmodulin: crystallographic and spectroscopic studies.
Authors: Vertessy, B.G. / Harmat, V. / Bocskei, Z. / Naray-Szabo, G. / Orosz, F. / Ovadi, J.
#1: Journal: Biochemistry / Year: 1994
Title: Drug Binding by Calmodulin: Crystal Structure of a Calmodulin-Trifluoperazine Complex
Authors: Cook, W.J. / Walter, L.J. / Walter, M.R.
History
DepositionJan 19, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _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

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6977
Polymers16,7211
Non-polymers9756
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.750, 40.750, 177.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CALMODULIN /


Mass: 16721.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cellular location: CYTOPLASM / Organ: BRAIN / References: UniProt: P62157
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TFP / 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE / Trifluoperazine


Mass: 407.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24F3N3S / Comment: antipsychotic*YM

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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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED BY SITTING DROP TECHNIQUE IN THE COLD ROOM (8 DEGREES C +/- 2 DEGREES C) BY MIXING 4 MICROLITERS OF 1 MM PROTEIN CONTAINING 1.2-1.5 MM TFP IN 5 MM CACL2 WITH 4 ...Details: PROTEIN WAS CRYSTALLIZED BY SITTING DROP TECHNIQUE IN THE COLD ROOM (8 DEGREES C +/- 2 DEGREES C) BY MIXING 4 MICROLITERS OF 1 MM PROTEIN CONTAINING 1.2-1.5 MM TFP IN 5 MM CACL2 WITH 4 MICROLITERS OF THE RESERVOIR SOLUTION (1 ML 10 MM SODIUM CACODYLATE/HCL BUFFER, PH 5.2-5.6 WITH 10 MM CACL2, 25-30 % (W/V) POLYETHYLENE GLYCOL 6000), CRYSTAL GROWTH TOOK 2-3 WEEKS., pH 5.0
Temp details: cold room (8 +/-2 C)
Crystal grow
*PLUS
Temperature: 6-10 ℃ / pH: 5.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
21.2-1.7 mMtrifluoperazine1drop
35 mM1dropCaCl2
410 mMsodium cacodylate-HCl1reservoir
510 mM1reservoirCaCl2
630 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1995 / Details: NORMAL FOCUS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.74→87.7 Å / Num. obs: 17223 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 1.92 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.0737 / Net I/σ(I): 11.3
Reflection shellResolution: 2.74→2.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 1.84 / Rsym value: 0.205 / % possible all: 98.2
Reflection
*PLUS
Num. obs: 5036 / % possible obs: 95.1 % / Num. measured all: 12467 / Rmerge(I) obs: 0.0737

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
bioteXdata reduction
bioteXdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIN
Resolution: 2.74→59.19 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 230 4.8 %RANDOM
Rwork0.1971 ---
obs0.1971 4768 96.46 %-
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--9.975 Å2-8.454 Å20 Å2
2---9.975 Å20 Å2
3----7.101 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.74→59.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 60 0 1147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
LS refinement shellResolution: 2.74→2.82 Å / Rfactor Rfree error: 0.098 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3395 12 4.9 %
Rwork0.1661 233 -
obs--57.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2CA.PARCA.TOP
X-RAY DIFFRACTION3TFP.PARTFP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor Rfree: 0.2654
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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