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- PDB-1u5q: Crystal Structure of the TAO2 Kinase Domain: Activation and Speci... -

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Basic information

Entry
Database: PDB / ID: 1u5q
TitleCrystal Structure of the TAO2 Kinase Domain: Activation and Specifity of a Ste20p MAP3K
Componentsserine/threonine protein kinase TAO2Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / serine/threonine protein kinase
Function / homology
Function and homology information


basal dendrite morphogenesis / basal dendrite arborization / positive regulation of stress-activated MAPK cascade / neuropilin binding / focal adhesion assembly / regulation of postsynapse organization / mitogen-activated protein kinase kinase binding / regulation of synaptic membrane adhesion / mitotic G2 DNA damage checkpoint signaling / dendritic growth cone ...basal dendrite morphogenesis / basal dendrite arborization / positive regulation of stress-activated MAPK cascade / neuropilin binding / focal adhesion assembly / regulation of postsynapse organization / mitogen-activated protein kinase kinase binding / regulation of synaptic membrane adhesion / mitotic G2 DNA damage checkpoint signaling / dendritic growth cone / regulation of MAPK cascade / MAP kinase kinase kinase activity / stress-activated MAPK cascade / axonal growth cone / axonogenesis / neuron projection morphogenesis / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / cytoplasmic vesicle membrane / MAPK cascade / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / postsynapse / positive regulation of MAPK cascade / cytoskeleton / receptor complex / non-specific serine/threonine protein kinase / neuron projection / axon / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / DNA damage response / ATP binding / cytoplasm
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase TAO2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhou, T. / Raman, M. / Gao, Y. / Earnest, S. / Chen, Z. / Machius, M. / Cobb, M.H. / Goldsmith, E.J.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal Structure of the TAO2 Kinase Domain; Activation and Specificity of a Ste20p MAP3K.
Authors: Zhou, T. / Raman, M. / Gao, Y. / Earnest, S. / Chen, Z. / Machius, M. / Cobb, M.H. / Goldsmith, E.J.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: serine/threonine protein kinase TAO2
B: serine/threonine protein kinase TAO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9014
Polymers79,8212
Non-polymers802
Water7,819434
1
A: serine/threonine protein kinase TAO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9512
Polymers39,9101
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: serine/threonine protein kinase TAO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9512
Polymers39,9101
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: serine/threonine protein kinase TAO2
hetero molecules

A: serine/threonine protein kinase TAO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9014
Polymers79,8212
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area1860 Å2
ΔGint-43 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.220, 186.220, 94.506
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein serine/threonine protein kinase TAO2 / Serine/threonine-specific protein kinase


Mass: 39910.469 Da / Num. of mol.: 2 / Fragment: N-terminal Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: serine/threonine protein kinase TAO2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q9JLS3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 3.006 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Imidazole, PEG 1000, calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.96417 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96417 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 56538 / Num. obs: 54996 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rsym value: 0.045 / Net I/σ(I): 30
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4 / % possible all: 98.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: The peptide bond Sep181 - Phe182 in both chains is 2.1 - 2.3 A long.
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 2783 -Random
Rwork0.2227 ---
all-54996 --
obs-54996 97.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.587 Å2-3.179 Å20 Å2
2---3.587 Å20 Å2
3---7.174 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 2 434 5416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.70666
X-RAY DIFFRACTIONc_bond_d0.013327
LS refinement shellResolution: 2.1→2.11 Å
RfactorNum. reflection
Rfree0.2907 51
Rwork0.2936 -
obs-966

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