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- PDB-5dyj: Mysosin heavy chain kinase A catalytic domain mutant - D663A -

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Basic information

Entry
Database: PDB / ID: 5dyj
TitleMysosin heavy chain kinase A catalytic domain mutant - D663A
ComponentsMyosin heavy chain kinase A
KeywordsTRANSFERASE / 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
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
Authorsvan Staalduinen, L.M. / Yang, Y. / Jia, Z.
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
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _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

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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)70,23610
Polymers69,0372
Non-polymers1,1998
Water1,820101
1
A: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1185
Polymers34,5181
Non-polymers6004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1185
Polymers34,5181
Non-polymers6004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.140, 110.250, 79.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 34518.371 Da / Num. of mol.: 2 / Fragment: UNP residues 552-841 / Mutation: D663A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhkA, mhckA, DDB_G0291231 / Production host: Escherichia coli (E. coli) / References: UniProt: P42527, myosin-heavy-chain kinase

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Non-polymers , 5 types, 109 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000, Sodium phosphate, Tris, Dichloromethane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 26125 / % possible obs: 99.7 % / Redundancy: 14.3 % / Rsym value: 0.122 / Net I/σ(I): 16.74
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 5.12 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3LLA

3lla


Resolution: 2.5→19.994 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1307 5.01 %Random
Rwork0.1847 ---
obs0.187 26106 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 70 101 4206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0234201
X-RAY DIFFRACTIONf_angle_d0.6825670
X-RAY DIFFRACTIONf_dihedral_angle_d11.0242523
X-RAY DIFFRACTIONf_chiral_restr0.045628
X-RAY DIFFRACTIONf_plane_restr0.004709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.59990.30551430.2432716X-RAY DIFFRACTION100
2.5999-2.71790.26351430.22222711X-RAY DIFFRACTION100
2.7179-2.86090.28691420.22232695X-RAY DIFFRACTION100
2.8609-3.03950.28151450.22222739X-RAY DIFFRACTION100
3.0395-3.27330.26321440.21532729X-RAY DIFFRACTION100
3.2733-3.60090.23551440.19382745X-RAY DIFFRACTION100
3.6009-4.1180.24561460.16922763X-RAY DIFFRACTION100
4.118-5.17340.1941460.14832783X-RAY DIFFRACTION100
5.1734-19.99450.18921540.16922918X-RAY DIFFRACTION100

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