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- PDB-2aao: Regulatory apparatus of Calcium Dependent protein kinase from Ara... -

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Basic information

Entry
Database: PDB / ID: 2aao
TitleRegulatory apparatus of Calcium Dependent protein kinase from Arabidopsis thaliana
ComponentsCalcium-dependent protein kinase, isoform AK1
KeywordsTRANSFERASE / Calcium dependent protein kinase / calmodulin-like domain / EF hand / Calcium binding protein
Function / homology
Function and homology information


: / regulation of leaf senescence / : / calcium-dependent protein serine/threonine kinase activity / peroxisomal membrane / peroxisome / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / calmodulin binding ...: / regulation of leaf senescence / : / calcium-dependent protein serine/threonine kinase activity / peroxisomal membrane / peroxisome / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
EF hand / 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 ...EF hand / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium-dependent protein kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsChandran, V. / Stollar, E.J. / Lindorff-Larsen, K. / Harper, J.F. / Chazin, W.J. / Dobson, C.M. / Luisi, B.F. / Christodoulou, J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition.
Authors: Chandran, V. / Stollar, E.J. / Lindorff-Larsen, K. / Harper, J.F. / Chazin, W.J. / Dobson, C.M. / Luisi, B.F. / Christodoulou, J.
History
DepositionJul 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent protein kinase, isoform AK1
B: Calcium-dependent protein kinase, isoform AK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,71311
Polymers38,3532
Non-polymers3619
Water2,756153
1
A: Calcium-dependent protein kinase, isoform AK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3375
Polymers19,1761
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium-dependent protein kinase, isoform AK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3776
Polymers19,1761
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-139 kcal/mol
Surface area14580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)35.968, 88.154, 117.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calcium-dependent protein kinase, isoform AK1 / CDPK


Mass: 19176.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AK1 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q06850, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.45 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG400, calcium chloride, sodium acetate , pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9766, 0.9795, 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97661
20.97951
30.951
ReflectionResolution: 2→20 Å / Num. obs: 25329 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.5
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 2.6 / % possible all: 86.7

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Processing

Software
NameVersionClassificationNB
REFMAC5refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→14.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.98 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1239 5.1 %RANDOM
Rwork0.213 ---
all0.215 26003 --
obs0.278 24445 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 9 153 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222311
X-RAY DIFFRACTIONr_bond_other_d0.0010.022058
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9633092
X-RAY DIFFRACTIONr_angle_other_deg0.81834825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5613283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32115453
X-RAY DIFFRACTIONr_chiral_restr0.0760.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_nbd_refined0.2760.3727
X-RAY DIFFRACTIONr_nbd_other0.220.32090
X-RAY DIFFRACTIONr_nbtor_other0.0910.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.5165
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1270.53
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.535
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4460.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.58
X-RAY DIFFRACTIONr_mcbond_it1.3831417
X-RAY DIFFRACTIONr_mcangle_it2.24242254
X-RAY DIFFRACTIONr_scbond_it1.6893894
X-RAY DIFFRACTIONr_scangle_it2.5544838
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 78 -
Rwork0.235 1305 -
all-1383 -
obs-1305 75.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.0499-7.575817.697510.9345-8.791731.06450.8958-0.0714-0.47030.7851-0.11030.42311.9926-0.7357-0.78550.4534-0.1393-0.0090.1579-0.02470.142420.3930.81541.59
21.50170.0883-0.06996.18432.48642.8708-0.0845-0.00640.0148-0.27710.0093-0.2922-0.24370.01540.07520.1246-0.0138-0.01870.30460.02660.276223.40528.94219.656
372.9271-63.8419-7.588449.4630.3423-2.17570.28820.74193.89390.2206-0.7149-4.1722-0.66780.38690.42670.12510.0286-0.17160.2230.03260.661736.16933.08522.865
45.6817-0.2362-1.03394.34370.882.6874-0.2202-0.2788-0.05470.28330.1174-0.31920.19390.10890.10280.07370.0292-0.04320.2841-0.01120.266927.12423.47927.653
58.14920.7173-0.321516.82130.78277.52010.15430.1487-0.03430.42530.0553-1.04960.42060.5625-0.20960.01730.019-0.04240.1932-0.03430.104928.39936.32730.176
62.0644-0.2266-1.34734.62741.61198.56750.07930.28710.1336-0.6647-0.10550.3259-0.3446-0.54850.02610.20520.1071-0.05380.28520.01570.181715.74344.30814.911
72.2083-0.8088-0.0395.62240.672317.68630.1699-0.00410.1843-0.9343-0.1546-0.5338-1.48970.2983-0.01530.39210.00140.0740.21510.05610.171626.16847.26111.768
84.11964.264-7.412413.2024-16.073735.81770.34180.3222-0.0327-0.3299-0.1530.1415-1.7233-0.6799-0.18870.33140.09980.00540.274-0.06230.159417.15451.11424.149
91.53150.6639-0.00064.99621.2692.66870.0423-0.08120.0720.2932-0.1566-0.16980.199-0.07240.11430.16430.0155-0.00380.28770.03580.231826.51753.53844.403
1055.626853.8299-24.660767.9973-42.655124.8609-0.4486-0.0749-2.0665-0.8336-0.8377-2.57220.78160.91481.28630.13130.02450.06960.2085-0.00920.335437.99449.24438.06
112.68340.3725-1.08893.3320.7450.1789-0.11320.25130.1996-0.14760.0274-0.03440.1371-0.04130.08570.1235-0.0297-0.0130.32110.02570.251927.65458.26935.288
127.33719.5065-11.425322.0788-7.426413.4315-0.0112-0.4901-0.81290.0724-0.3116-0.749-0.28140.57260.32280.017-0.0226-0.03380.1703-0.00590.103329.16346.38333.388
133.6082-2.5393.30674.9565.12578.3522-0.0142-0.4628-0.25170.6973-0.01090.40170.3602-0.58730.02510.3417-0.07710.07020.2050.050.127721.07339.16350.343
144.5021.62692.58953.2311-0.972910.40570.00210.0458-0.16540.35710.3236-0.3841.16170.2797-0.32560.45770.0515-0.03490.1771-0.01940.134631.21636.67451.485
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 236 - 23
22AA24 - 5624 - 56
33AA57 - 6157 - 61
44AA62 - 9062 - 90
55AA91 - 9991 - 99
66AA100 - 127100 - 127
77AA136 - 160136 - 160
88BB6 - 236 - 23
99BB24 - 5624 - 56
1010BB57 - 6157 - 61
1111BB62 - 9062 - 90
1212BB91 - 9991 - 99
1313BB100 - 123100 - 123
1414BB140 - 160140 - 160

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