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- PDB-1uix: Coiled-coil structure of the RhoA-binding domain in Rho-kinase -

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Basic information

Entry
Database: PDB / ID: 1uix
TitleCoiled-coil structure of the RhoA-binding domain in Rho-kinase
ComponentsRho-associated kinase
KeywordsTRANSFERASE / coiled-coil
Function / homology
Function and homology information


positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization ...positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization / regulation of circadian rhythm / small GTPase binding / rhythmic process / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single helix bin / : / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type profile. ...Single helix bin / : / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-like domain superfamily / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho-associated protein kinase 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsShimizu, T. / Ihara, K. / Maesaki, R. / Amano, M. / Kaibuchi, K. / Hakoshima, T.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Parallel coiled-coil association of the RhoA-binding domain in Rho-kinase
Authors: Shimizu, T. / Ihara, K. / Maesaki, R. / Amano, M. / Kaibuchi, K. / Hakoshima, T.
History
DepositionJul 23, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-associated kinase
B: Rho-associated kinase


Theoretical massNumber of molelcules
Total (without water)16,1122
Polymers16,1122
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-36 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.0, 26.1, 39.6
Angle α, β, γ (deg.)90, 90.4, 90
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer

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Components

#1: Protein Rho-associated kinase / coiled-coil domain in Rho-kinase


Mass: 8055.914 Da / Num. of mol.: 2 / Fragment: coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: UniProt: Q28021, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.32 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, KCl, PEG1000, ethylene glycol, n-octanoylsucrose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Thara, K., (2000) Acta Crystallogr., D56, 1042.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.7 mg/mlprotein1drop
255 mMHEPES1droppH7.0
323 mM1dropKCl
411 %PEG10001drop
514 %ethylene glycol1drop
622 mMn-octanoylsucrose1drop
7100 mMHEPES1reservoirpH7.0
825 %PEG10001reservoir
930 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9784, 0.9778, 0.9600, 1.000
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 15, 1999
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97841
20.97781
30.961
411
ReflectionResolution: 1.8→39.53 Å / Num. all: 12896 / Num. obs: 12896 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 14.8 / % possible all: 68.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 139215
Reflection shell
*PLUS
% possible obs: 68.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.5 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1283 10 %RANDOM
Rwork0.193 ---
all0.219 12896 --
obs0.219 12894 89.1 %-
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20.37 Å2
2--0.8 Å20 Å2
3----0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 174 1175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_mcbond_it1.034
X-RAY DIFFRACTIONr_mcangle_it1.833
X-RAY DIFFRACTIONr_scbond_it3.49
X-RAY DIFFRACTIONr_scangle_it5.229
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 56
Rwork0.148 647
Refinement
*PLUS
Highest resolution: 1.8 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.511
X-RAY DIFFRACTIONr_improper_angle_d
X-RAY DIFFRACTIONr_improper_angle_deg1.713

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