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- PDB-3lkm: 1.6 Angstrom Crystal Structure of the Alpha-kinase Domain of Myos... -

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Basic information

Entry
Database: PDB / ID: 3lkm
Title1.6 Angstrom Crystal Structure of the Alpha-kinase Domain of Myosin Heavy Chain Kinase A Complex with AMP
ComponentsMyosin heavy chain kinase A
KeywordsTRANSFERASE / Protein Kinase-like fold / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Alpha-kinase / Coiled coil / WD repeat
Function / homology
Function and homology information


myosin-heavy-chain kinase / myosin heavy chain kinase activity / myosin II filament disassembly / ADP phosphatase activity / actomyosin contractile ring / actin crosslink formation / myosin II binding / AMP binding / actin filament bundle assembly / mitotic cytokinesis ...myosin-heavy-chain kinase / myosin heavy chain kinase activity / myosin II filament disassembly / ADP phosphatase activity / actomyosin contractile ring / actin crosslink formation / myosin II binding / AMP binding / actin filament bundle assembly / mitotic cytokinesis / cAMP binding / ADP binding / chemotaxis / actin filament binding / cell cortex / protein autophosphorylation / protein kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Protein kinase-like fold / MHCK/EF2 kinase / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat ...Protein kinase-like fold / MHCK/EF2 kinase / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Barrel / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsYe, Q. / Jia, Z.
CitationJournal: Sci.Signal. / Year: 2010
Title: Crystal Structure of the {alpha}-Kinase Domain of Dictyostelium Myosin Heavy Chain Kinase A.
Authors: Ye, Q. / Crawley, S.W. / Yang, Y. / Cote, G.P. / Jia, Z.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2028
Polymers34,5271
Non-polymers6757
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.224, 83.777, 44.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin heavy chain kinase A / MHCK-A


Mass: 34526.582 Da / Num. of mol.: 1 / Fragment: UNP residues 552-841
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX3 / Gene: DDB_G0291231, mhckA, mhkA / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42527, myosin-heavy-chain kinase

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Non-polymers , 5 types, 312 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M potassium phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONCHESS F110.918
ROTATING ANODERIGAKU MICROMAX-007 HF22.29
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 11CCDApr 18, 2007
RIGAKU RAXIS IV2IMAGE PLATEMar 22, 2007Cr VariMax Multilayer Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9181
22.291
ReflectionResolution: 1.6→50 Å / Num. obs: 37007 / % possible obs: 96.6 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 46.52
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 9.77 / % possible all: 78.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→28.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.357 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 1849 5 %RANDOM
Rwork0.19364 ---
obs0.19507 34910 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.733 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 37 305 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222039
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9892755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79925.34188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6615373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.66157
X-RAY DIFFRACTIONr_chiral_restr0.0730.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211498
X-RAY DIFFRACTIONr_mcbond_it0.5911.51228
X-RAY DIFFRACTIONr_mcangle_it1.15521988
X-RAY DIFFRACTIONr_scbond_it1.7453811
X-RAY DIFFRACTIONr_scangle_it2.9184.5767
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 103 -
Rwork0.212 1941 -
obs--73.42 %

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