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- PDB-1jad: C-terminal Domain of Turkey PLC-beta -

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Basic information

Entry
Database: PDB / ID: 1jad
TitleC-terminal Domain of Turkey PLC-beta
Componentsphospholipase C beta
KeywordsHYDROLASE / AlPHA HELICAL COILED COIL
Function / homology
Function and homology information


phosphoinositide phospholipase C / phosphatidylinositol phospholipase C activity / lipid catabolic process / intracellular signal transduction / calcium ion binding / cytosol
Similarity search - Function
Phospholipase C Beta; Chain: A / Phospholipase C beta, distal C-terminal domain / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain ...Phospholipase C Beta; Chain: A / Phospholipase C beta, distal C-terminal domain / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsSinger, A.U. / Waldo, G.L. / Harden, T.K. / Sondek, J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: A unique fold of phospholipase C-beta mediates dimerization and interaction with G alpha q.
Authors: Singer, A.U. / Waldo, G.L. / Harden, T.K. / Sondek, J.
History
DepositionMay 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phospholipase C beta
B: phospholipase C beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7763
Polymers59,6802
Non-polymers961
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.111, 51.928, 79.350
Angle α, β, γ (deg.)101.07, 96.96, 100.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2981, 0.2383, 0.9243), (0.2397, -0.956, 0.1691), (0.9239, 0.1711, -0.3421)
Vector: -36.2667, 51.7161, 36.9613)

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Components

#1: Protein phospholipase C beta / PLC-BETA


Mass: 29840.090 Da / Num. of mol.: 2 / Fragment: C-terminus / Mutation: DEL(946-978)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Cell: erythrocyte / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q91086, phosphoinositide phospholipase C
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 2000, bis-tris, lithium sulfate, glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
PH range low: 6.3 / PH range high: 5.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-16 %(w/v)PEG20001reservoir
280 mMBis-Tris1reservoirpH5.7-6.3
360-120 mMammonium sulfate1reservoir
410 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97949, 0.97940, 0.97526
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.97941
30.975261
ReflectionResolution: 2.4→30 Å / Num. all: 22737 / Num. obs: 20867 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 31.8 Å2 / Limit h max: 18 / Limit h min: -18 / Limit k max: 23 / Limit k min: -18 / Limit l max: 37 / Limit l min: 0 / Observed criterion F max: 2383914.3 / Observed criterion F min: 48.1 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 6.2 / Num. unique all: 873 / Rsym value: 0.2 / % possible all: 75.1

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Processing

Software
NameVersionClassificationNB
CNS1refinement
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1061 5.1 %random
Rwork0.254 ---
all0.256 20931 --
obs0.256 20931 90.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 29.7183 Å2 / ksol: 0.335158 e/Å3
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 43.04 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-6 Å210 Å27.16 Å2
2---9.37 Å2-4.68 Å2
3---3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 5 143 4156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.25
X-RAY DIFFRACTIONx_dihedral_angle_d14.8
X-RAY DIFFRACTIONx_improper_angle_d0.73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.3411133.90.31320970.0292890221076.5
2.51-2.640.2931093.80.29222780.0282906238782.1
2.64-2.810.2911334.50.28923890.0252946252285.6
2.81-3.020.2891294.50.28824510.0252880258089.6
3.02-3.330.251334.60.25125870.0222893272094
3.33-3.810.2371364.70.2426910.022909282797.2
3.81-4.790.2141735.90.21526770.0162909285098
4.79-28.070.2511374.70.24827230.0212902286098.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.254 / Rfactor Rfree: 0.293
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.313

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