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- PDB-4zs4: Crystal Structure of the Inactive Alpha-kinase Domain of Myosin-I... -

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Basic information

Entry
Database: PDB / ID: 4zs4
TitleCrystal Structure of the Inactive Alpha-kinase Domain of Myosin-II Heavy Chain Kinase A (D756A) Complexed with ATP
ComponentsMyosin heavy chain kinase A
KeywordsTRANSFERASE / Protein kinase like fold / Atypical Ser/Thr protein kinases
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-5'-TRIPHOSPHATE / PHOSPHATE ION / Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsYe, Q. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Characterization of the Catalytic and Nucleotide Binding Properties of the alpha-Kinase Domain of Dictyostelium Myosin-II Heavy Chain Kinase A.
Authors: Yang, Y. / Ye, Q. / Jia, Z. / Cote, G.P.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jun 1, 2016Group: Data collection
Revision 1.3Jan 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 1.4Sep 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

Downloads & links

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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)70,3008
Polymers68,9652
Non-polymers1,3356
Water5,801322
1
A: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1504
Polymers34,4831
Non-polymers6683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1504
Polymers34,4831
Non-polymers6683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.207, 109.744, 77.845
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: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 552 - 806 / Label seq-ID: 18 - 272

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

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Components

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


Mass: 34482.570 Da / Num. of mol.: 2 / Fragment: residues 552-841 / Mutation: D756A
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42527, myosin-heavy-chain kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.75 / Details: PEG 3350, lithium sulphate, Tris chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97938 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 28026 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.14 / Χ2: 1.542 / Net I/σ(I): 17.826 / Num. measured all: 227342
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.4-2.444.30.5492.70411851.23399.5
2.64-2.696.40.48611420.995100
2.69-2.746.90.49111791.008100
2.74-2.87.30.44611651.039100
2.8-2.867.80.41611761.164100
2.86-2.938.50.43111961.205100
2.93-390.41911501.309100
3-3.089.60.36811791.381100
3.08-3.1710.10.3611981.445100
3.17-3.2810.60.33611811.389100
3.28-3.39110.27311711.432100
3.39-3.5311.10.21911891.525100
3.53-3.6911.10.16411781.46100
3.69-3.88110.14311991.436100
3.88-4.12110.1211991.589100
4.12-4.44110.11211901.827100
4.44-4.8910.90.09512102.085100
4.89-5.5910.80.08612291.805100
5.59-7.0310.60.08312331.941100
7.03-309.80.06213152.466100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHASER2.1.4phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKM

3lkm


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.777 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1411 5 %RANDOM
Rwork0.1785 ---
obs0.1808 26549 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.96 Å2 / Biso mean: 36.069 Å2 / Biso min: 14.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å2-0 Å2
2--1.34 Å2-0 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 74 322 4428
Biso mean--37.4 38.39 -
Num. residues----510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194191
X-RAY DIFFRACTIONr_bond_other_d0.0040.024036
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.995669
X-RAY DIFFRACTIONr_angle_other_deg0.97739340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89625.314175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10615765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7651514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214591
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02905
X-RAY DIFFRACTIONr_mcbond_it2.4913.3872035
X-RAY DIFFRACTIONr_mcbond_other2.493.3862034
X-RAY DIFFRACTIONr_mcangle_it4.2295.0572535
Refine LS restraints NCS

Ens-ID: 1 / Number: 14675 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 64 -
Rwork0.274 1212 -
all-1276 -
obs--60.62 %

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