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- PDB-5e9e: Crystal Structure of the Alpha-kinase Domain of Myosin-II Heavy C... -

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Basic information

Entry
Database: PDB / ID: 5e9e
TitleCrystal Structure of the Alpha-kinase Domain of Myosin-II Heavy Chain Kinase A in Complex with AMP-PNP
ComponentsMyosin-II heavy chain kinase A
KeywordsTRANSFERASE / atypical Ser/Thr protein kinase / alpha kinase
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYe, Q. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Rep / Year: 2016
Title: Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (MHCK-A) alpha-kinase domain apoenzyme reveals a novel autoinhibited conformation.
Authors: Ye, Q. / Yang, Y. / van Staalduinen, L. / Crawley, S.W. / Liu, L. / Brennan, S. / Cote, G.P. / Jia, Z.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,3868
Polymers69,0532
Non-polymers1,3336
Water3,837213
1
A: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1934
Polymers34,5271
Non-polymers6673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1934
Polymers34,5271
Non-polymers6673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.601, 110.112, 78.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 552 - 810 / Label seq-ID: 18 - 276

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 34526.582 Da / Num. of mol.: 2 / Fragment: alpha kinase domain (UNP residues 552-841)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhkA, mhckA, DDB_G0291231 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42527, myosin-heavy-chain kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*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 / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG8000, 0.1 M MOPS, 0.2 M magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 24, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 28601 / Num. obs: 28345 / % possible obs: 97.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.123 / Net I/av σ(I): 4.67 / Net I/σ(I): 23.53
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.349 / % possible all: 86.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-20001.98.7data reduction
HKL-20001.98.7data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LMH

3lmh


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.311 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 1434 5.1 %RANDOM
Rwork0.1913 ---
obs0.1936 26910 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.9 Å2 / Biso mean: 42.823 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å2-0 Å2-0 Å2
2--0.96 Å2-0 Å2
3---1.85 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 74 213 4365
Biso mean--46.54 39.81 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.010.01942370.07
X-RAY DIFFRACTIONr_bond_other_d0.0040.024086
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.99257260.07
X-RAY DIFFRACTIONr_angle_other_deg0.94739459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28525.419179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31515778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9211514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214639
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02913
X-RAY DIFFRACTIONr_mcbond_it2.7534.0932055
X-RAY DIFFRACTIONr_mcbond_other2.7534.0922054
X-RAY DIFFRACTIONr_mcangle_it4.4996.1132557
Refine LS restraints NCS

Ens-ID: 1 / Number: 15167 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 97 -
Rwork0.231 1942 -
all-2039 -
obs--98.31 %

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