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- PDB-3lmi: Crystal Structure of the Inactive Alpha-kinase Domain of Myosin H... -

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Basic information

Entry
Database: PDB / ID: 3lmi
TitleCrystal Structure of the Inactive Alpha-kinase Domain of Myosin Heavy Chain Kinase A (D766A) complex with ATP
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 / mitotic cytokinesis / actin filament bundle assembly ...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 / mitotic cytokinesis / actin filament bundle assembly / cAMP binding / ADP binding / chemotaxis / actin filament binding / cell cortex / 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. ...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 / Phosphorylase Kinase; domain 1 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Phosphorylase Kinase; domain 1 / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / 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-5'-TRIPHOSPHATE / PHOSPHATE ION / Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Myosin heavy chain kinase A
C: Myosin heavy chain kinase A
D: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,88822
Polymers137,9304
Non-polymers2,95718
Water10,287571
1
A: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1745
Polymers34,4831
Non-polymers6924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2696
Polymers34,4831
Non-polymers7875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1745
Polymers34,4831
Non-polymers6924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2696
Polymers34,4831
Non-polymers7875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.192, 81.192, 187.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 34482.570 Da / Num. of mol.: 4 / Fragment: UNP residues 552-841 / Mutation: D766A
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, 589 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 56572 / % possible obs: 92.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.63
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 6.723 / % possible all: 80.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC6.1.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LKM

3lkm


Resolution: 2.2→29.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.869 / SU B: 5.701 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26916 2863 5.1 %RANDOM
Rwork0.19908 ---
obs0.20257 53661 92.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.452 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7956 0 162 571 8689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.99411194
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.825.246345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.942151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8721528
X-RAY DIFFRACTIONr_chiral_restr0.0840.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7011.54985
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32628074
X-RAY DIFFRACTIONr_scbond_it1.78933293
X-RAY DIFFRACTIONr_scangle_it3.0014.53120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 201 -
Rwork0.189 3478 -
obs--80.59 %

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