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- PDB-3lmh: Crystal Structure of the Alpha-kinase Domain of Myosin Heavy Chai... -

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Basic information

Entry
Database: PDB / ID: 3lmh
TitleCrystal Structure of the Alpha-kinase Domain of Myosin Heavy Chain Kinase A Complex with ADP
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. ...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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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'-DIPHOSPHATE / PHOSPHATE ION / Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: Myosin heavy chain kinase A
B: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3888
Polymers69,2132
Non-polymers1,1756
Water6,630368
1
A: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1944
Polymers34,6071
Non-polymers5883
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)35,1944
Polymers34,6071
Non-polymers5883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.824, 110.047, 78.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 34606.559 Da / Num. of mol.: 2 / 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, mnkA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42527, myosin-heavy-chain kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3350, 0.2M magnesium sulfate, 0.1M cacodylate , pH 6.0, 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: Jun 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 49217 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 32.01
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 4.803 / Num. unique all: 4880 / % possible all: 99.9

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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→19.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.917 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25924 2484 5.1 %RANDOM
Rwork0.21639 ---
obs0.21858 46631 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.827 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 66 368 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224044
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9965469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19125.176170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6721514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212944
X-RAY DIFFRACTIONr_mcbond_it0.7481.52427
X-RAY DIFFRACTIONr_mcangle_it1.41423932
X-RAY DIFFRACTIONr_scbond_it2.05231617
X-RAY DIFFRACTIONr_scangle_it3.4114.51537
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 205 -
Rwork0.269 3341 -
obs--99.72 %

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