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- PDB-5e4h: Crystal Structure of Apoenzyme Alpha-kinase Domain of Myosin-II H... -

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Basic information

Entry
Database: PDB / ID: 5e4h
TitleCrystal Structure of Apoenzyme Alpha-kinase Domain of Myosin-II Heavy Chain Kinase A
ComponentsMyosin-II heavy chain kinase A
KeywordsTRANSFERASE / alpha kinase / ePK domain fold
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
Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYe, Q. / Cote, G.P. / Jia, Z.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
The Natural Sciences and Engineering Research Council of Canada 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 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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-II heavy chain kinase A
B: Myosin-II heavy chain kinase A
C: Myosin-II heavy chain kinase A
D: Myosin-II heavy chain kinase A
E: Myosin-II heavy chain kinase A
F: Myosin-II heavy chain kinase A
G: Myosin-II heavy chain kinase A
H: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,01616
Polymers277,4928
Non-polymers5238
Water1,15364
1
A: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,6871
Non-polymers651
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)34,7522
Polymers34,6871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,6871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,6871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,6871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,6871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,6871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Myosin-II heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7522
Polymers34,6871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.298, 103.469, 167.811
Angle α, β, γ (deg.)90.000, 89.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA554 - 80820 - 274
21SERSERLYSLYSBB554 - 80820 - 274
12THRTHRASPASPAA556 - 80622 - 272
22THRTHRASPASPCC556 - 80622 - 272
13SERSERLEULEUAA553 - 80919 - 275
23SERSERLEULEUDD553 - 80919 - 275
14SERSERVALVALAA554 - 80720 - 273
24SERSERVALVALEE554 - 80720 - 273
15SERSERLYSLYSAA553 - 80819 - 274
25SERSERLYSLYSFF553 - 80819 - 274
16SERSERLEULEUAA553 - 80919 - 275
26SERSERLEULEUGG553 - 80919 - 275
17GLUGLUVALVALAA555 - 80721 - 273
27GLUGLUVALVALHH555 - 80721 - 273
18THRTHRASPASPBB556 - 80622 - 272
28THRTHRASPASPCC556 - 80622 - 272
19SERSERLYSLYSBB554 - 80820 - 274
29SERSERLYSLYSDD554 - 80820 - 274
110SERSERLYSLYSBB554 - 80820 - 274
210SERSERLYSLYSEE554 - 80820 - 274
111SERSERLYSLYSBB554 - 80820 - 274
211SERSERLYSLYSFF554 - 80820 - 274
112SERSERLYSLYSBB554 - 80820 - 274
212SERSERLYSLYSGG554 - 80820 - 274
113GLUGLULYSLYSBB555 - 80821 - 274
213GLUGLULYSLYSHH555 - 80821 - 274
114THRTHRASPASPCC556 - 80622 - 272
214THRTHRASPASPDD556 - 80622 - 272
115THRTHRASPASPCC556 - 80622 - 272
215THRTHRASPASPEE556 - 80622 - 272
116THRTHRASPASPCC556 - 80622 - 272
216THRTHRASPASPFF556 - 80622 - 272
117THRTHRASPASPCC556 - 80622 - 272
217THRTHRASPASPGG556 - 80622 - 272
118THRTHRVALVALCC556 - 80722 - 273
218THRTHRVALVALHH556 - 80722 - 273
119SERSERLYSLYSDD554 - 80820 - 274
219SERSERLYSLYSEE554 - 80820 - 274
120ILEILELEULEUDD552 - 80918 - 275
220ILEILELEULEUFF552 - 80918 - 275
121ILEILELEULEUDD552 - 80918 - 275
221ILEILELEULEUGG552 - 80918 - 275
122GLUGLUVALVALDD555 - 80721 - 273
222GLUGLUVALVALHH555 - 80721 - 273
123SERSERVALVALEE554 - 80720 - 273
223SERSERVALVALFF554 - 80720 - 273
124SERSERLYSLYSEE554 - 80820 - 274
224SERSERLYSLYSGG554 - 80820 - 274
125GLUGLUVALVALEE555 - 80721 - 273
225GLUGLUVALVALHH555 - 80721 - 273
126ILEILELEULEUFF552 - 80918 - 275
226ILEILELEULEUGG552 - 80918 - 275
127GLUGLUVALVALFF555 - 80721 - 273
227GLUGLUVALVALHH555 - 80721 - 273
128GLUGLUVALVALGG555 - 80721 - 273
228GLUGLUVALVALHH555 - 80721 - 273

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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


Mass: 34686.539 Da / Num. of mol.: 8 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG8000, PEG300, glycerol, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2010
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 63388 / Num. obs: 61697 / % possible obs: 98.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.72
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.33 / % possible all: 86.4

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Processing

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

3lkm


Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 21.408 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3125 5.1 %RANDOM
Rwork0.2409 ---
obs0.2423 58572 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.86 Å2 / Biso mean: 79.993 Å2 / Biso min: 34.61 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å2-0 Å20.05 Å2
2--0.99 Å2-0 Å2
3----4.51 Å2
Refinement stepCycle: final / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15997 0 8 64 16069
Biso mean--73.84 54.33 -
Num. residues----2008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01916339
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215865
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9822069
X-RAY DIFFRACTIONr_angle_other_deg1.493336726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27651990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70525.212685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.878153018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2371556
X-RAY DIFFRACTIONr_chiral_restr0.0740.22433
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117998
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023518
X-RAY DIFFRACTIONr_mcbond_it4.0377.7848014
X-RAY DIFFRACTIONr_mcbond_other4.0327.7848013
X-RAY DIFFRACTIONr_mcangle_it6.55211.6649986
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A137750.14
12B137750.14
21A136620.15
22C136620.15
31A145770.13
32D145770.13
41A139620.14
42E139620.14
51A144610.13
52F144610.13
61A145600.13
62G145600.13
71A139660.13
72H139660.13
81B141130.13
82C141130.13
91B143330.12
92D143330.12
101B144800.11
102E144800.11
111B141160.14
112F141160.14
121B140370.14
122G140370.14
131B143360.13
132H143360.13
141C141100.13
142D141100.13
151C143870.12
152E143870.12
161C139480.14
162F139480.14
171C141460.13
172G141460.13
181C145270.12
182H145270.12
191D143720.13
192E143720.13
201D149380.11
202F149380.11
211D149070.13
212G149070.13
221D142220.13
222H142220.13
231E141480.14
232F141480.14
241E143050.13
242G143050.13
251E145670.12
252H145670.12
261F147280.13
262G147280.13
271F142630.13
272H142630.13
281G143470.13
282H143470.13
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 201 -
Rwork0.413 3683 -
all-3884 -
obs--82.8 %

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