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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)
DescriptorCALMODULIN
10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE
KeywordsCALCIUM-BINDING PROTEIN
Specimen sourceBos taurus / mammal / cattle / ウシ /
MethodX-ray diffraction (2.74 Å resolution / Molecular replacement)
AuthorsBocskei, Zs. / Harmat, V. / Vertessy, B.G. / Ovadi, J. / Naray-Szabo, G.
CitationBiochemistry, 1998, 37, 15300-15310

primary. Biochemistry, 1998, 37, 15300-15310 Yorodumi Papers
Simultaneous binding of drugs with different chemical structures to Ca2+-calmodulin: crystallographic and spectroscopic studies.
Vertessy, B.G. / Harmat, V. / Bocskei, Z. / Naray-Szabo, G. / Orosz, F. / Ovadi, J.

#1. Biochemistry, 1994, 33, 15259-
Drug Binding by Calmodulin: Crystal Structure of a Calmodulin-Trifluoperazine Complex
Cook, W.J. / Walter, L.J. / Walter, M.R.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 1998 / Release: Sep 16, 1998
RevisionDateData content typeGroupProviderType
1.0Sep 16, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6977
Polyers16,7211
Non-polymers9756
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 32 2 1

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Components

#1: Polypeptide(L)CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P62157

Cellular component

Molecular function

Biological process

  • detection of calcium ion (GO: 0005513)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • G2/M transition of mitotic cell cycle (GO: 0000086)
  • muscle contraction (GO: 0006936)
  • negative regulation of ryanodine-sensitive calcium-release channel activity (GO: 0060315)
  • positive regulation of cAMP biosynthetic process (GO: 0030819)
  • positive regulation of cyclic-nucleotide phosphodiesterase activity (GO: 0051343)
  • positive regulation of DNA binding (GO: 0043388)
  • positive regulation of phosphoprotein phosphatase activity (GO: 0032516)
  • positive regulation of ryanodine-sensitive calcium-release channel activity (GO: 0060316)
  • regulation of cardiac muscle contraction (GO: 0055117)
  • regulation of heart rate (GO: 0002027)
  • regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO: 0010880)
  • regulation of rhodopsin mediated signaling pathway (GO: 0022400)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Formula: Ca
#3: ChemicalChemComp-TFP / 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE


Mass: 407.496 Da / Num. of mol.: 2 / Formula: C21H24F3N3S

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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 / Density percent 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 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
Temp: 6-10 / Temp unit: ℃ / pH: 5.2 / Method: Vapor diffusion, hanging drop
Crystal grow comp
*PLUS

Crystal ID: 1

IDConcConc unitCommon nameSol IDChemical formula
11mMproteindrop
21.2-1.7mMtrifluoperazinedrop
35mMdropCaCl2
410mMsodium cacodylate-HClreservoir
510mMreservoirCaCl2
630%(w/v)PEG6000reservoir

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Data collection

DiffractionMean temperature: 293 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Details: NORMAL FOCUS / Detector: IMAGE PLATE / Collection date: Feb 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 32 Å2 / D resolution high: 2.74 Å / D resolution low: 87.7 Å / Number obs: 17223 / Observed criterion sigma I: 1 / Rmerge I obs: 0.086 / Rsym value: 0.0737 / NetI over sigmaI: 11.3 / Redundancy: 1.92 / Percent possible obs: 98
Reflection shellRmerge I obs: 0.092 / Highest resolution: 2.74 Å / Lowest resolution: 2.86 Å / MeanI over sigI obs: 1.84 / Rsym value: 0.205 / Redundancy: 1.9 / Percent possible all: 98.2
Reflection
*PLUS
Number obs: 5036 / Number measured all: 12467 / Percent possible obs: 95.1 / 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
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIN
R Free selection details: RANDOM / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 30.3 Å2 / Aniso B11: -9.975 Å2 / Aniso B12: -8.454 Å2 / Aniso B13: 0 Å2 / Aniso B22: -9.975 Å2 / Aniso B23: 0 Å2 / Aniso B33: -7.101 Å2
Least-squares processR factor R free: 0.265 / R factor R free error: 0.017 / R factor R work: 0.1971 / R factor obs: 0.1971 / Highest resolution: 2.74 Å / Lowest resolution: 59.19 Å / Number reflection R free: 230 / Number reflection obs: 4768 / Percent reflection R free: 4.8 / Percent reflection obs: 96.46
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.22 Å / Luzzati sigma a obs: 0.12 Å
Refine hist #LASTHighest resolution: 2.74 Å / Lowest resolution: 59.19 Å
Number of atoms included #LASTProtein: 1087 / Nucleic acid: 0 / Ligand: 60 / Solvent: 0 / Total: 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_d1.10
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
Refine LS shellHighest resolution: 2.74 Å / R factor R free: 0.3395 / R factor R free error: 0.098 / R factor R work: 0.1661 / Lowest resolution: 2.82 Å / Number reflection R free: 12 / Number reflection R work: 233 / Total number of bins used: 8 / Percent reflection R free: 4.9 / Percent reflection 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
Refine
*PLUS
Sigma F: 2
Least-squares process
*PLUS
R factor R free: 0.2654
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_deg1.10

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