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- PDB-6mcp: L. pneumophila effector kinase LegK7 (AMP-PNP bound) in complex w... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6mcp
TitleL. pneumophila effector kinase LegK7 (AMP-PNP bound) in complex with human MOB1A
Components
  • LegK7
  • MOB kinase activator 1A
KeywordsTRANSFERASE / translocated effector / Ser/Thr protein kinase / allosteric activation / Hippo pathway
Function / homology
Function and homology information


hippo signaling / Signaling by Hippo / protein kinase activator activity / protein serine/threonine kinase activator activity / extracellular exosome / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / DI(HYDROXYETHYL)ETHER / Protein kinase domain containing protein / MOB kinase activator 1A
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBeyrakhova, K.A. / Xu, C. / Boniecki, M.T. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-48370 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: TheLegionellakinase LegK7 exploits the Hippo pathway scaffold protein MOB1A for allostery and substrate phosphorylation.
Authors: Lee, P.C. / Beyrakhova, K. / Xu, C. / Boniecki, M.T. / Lee, M.H. / Onu, C.J. / Grishin, A.M. / Machner, M.P. / Cygler, M.
History
DepositionSep 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Oct 11, 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.pdbx_dist_value / _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_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: LegK7
B: MOB kinase activator 1A
C: LegK7
D: MOB kinase activator 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,02233
Polymers164,7084
Non-polymers4,31429
Water1,964109
1
A: LegK7
B: MOB kinase activator 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,61017
Polymers82,3542
Non-polymers2,25615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint24 kcal/mol
Surface area31810 Å2
MethodPISA
2
C: LegK7
D: MOB kinase activator 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,41216
Polymers82,3542
Non-polymers2,05814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint4 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.860, 112.430, 155.220
Angle α, β, γ (deg.)90.000, 105.580, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 45 or (resid 46...
21(chain C and ((resid 11 through 12 and (name N...
12(chain B and (resid 32 through 37 or (resid 38...
22(chain D and (resid 32 or (resid 33 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSTHRTHR(chain A and (resid 11 through 45 or (resid 46...AA11 - 454 - 38
121GLNGLNLEULEU(chain A and (resid 11 through 45 or (resid 46...AA46 - 4739 - 40
131ALAALAASNASN(chain A and (resid 11 through 45 or (resid 46...AA10 - 5293 - 522
141ALAALAASNASN(chain A and (resid 11 through 45 or (resid 46...AA10 - 5293 - 522
151ALAALAASNASN(chain A and (resid 11 through 45 or (resid 46...AA10 - 5293 - 522
161ALAALAASNASN(chain A and (resid 11 through 45 or (resid 46...AA10 - 5293 - 522
211LYSLYSASNASN(chain C and ((resid 11 through 12 and (name N...CC11 - 124 - 5
221LYSLYSASNASN(chain C and ((resid 11 through 12 and (name N...CC11 - 5294 - 522
231LYSLYSASNASN(chain C and ((resid 11 through 12 and (name N...CC11 - 5294 - 522
241LYSLYSASNASN(chain C and ((resid 11 through 12 and (name N...CC11 - 5294 - 522
251LYSLYSASNASN(chain C and ((resid 11 through 12 and (name N...CC11 - 5294 - 522
112ALAALAGLYGLY(chain B and (resid 32 through 37 or (resid 38...BB32 - 373 - 8
122SERSERSERSER(chain B and (resid 32 through 37 or (resid 38...BB389
132ASNASNSERSER(chain B and (resid 32 through 37 or (resid 38...BB31 - 2132 - 184
142ASNASNSERSER(chain B and (resid 32 through 37 or (resid 38...BB31 - 2132 - 184
152ASNASNSERSER(chain B and (resid 32 through 37 or (resid 38...BB31 - 2132 - 184
162ASNASNSERSER(chain B and (resid 32 through 37 or (resid 38...BB31 - 2132 - 184
212ALAALAALAALA(chain D and (resid 32 or (resid 33 and (name...DD323
222GLUGLUGLUGLU(chain D and (resid 32 or (resid 33 and (name...DD334
232ALAALAGLYGLY(chain D and (resid 32 or (resid 33 and (name...DD32 - 2123 - 183
242ALAALAGLYGLY(chain D and (resid 32 or (resid 33 and (name...DD32 - 2123 - 183
252ALAALAGLYGLY(chain D and (resid 32 or (resid 33 and (name...DD32 - 2123 - 183
262ALAALAGLYGLY(chain D and (resid 32 or (resid 33 and (name...DD32 - 2123 - 183
272ALAALAGLYGLY(chain D and (resid 32 or (resid 33 and (name...DD32 - 2123 - 183

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein LegK7


Mass: 60684.215 Da / Num. of mol.: 2 / Fragment: UNP residues 11-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1924 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5ZU83, non-specific serine/threonine protein kinase
#2: Protein MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B


Mass: 21669.703 Da / Num. of mol.: 2 / Fragment: UNP residues 33-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H8S9

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Non-polymers , 7 types, 138 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#5: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 21% PEG600, 0.2 M sodium chloride, 20 mM succinate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 16, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→48.668 Å / Num. obs: 61056 / % possible obs: 99.8 % / Redundancy: 5.091 % / Biso Wilson estimate: 57.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.102 / Χ2: 0.975 / Net I/σ(I): 11.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.565.0080.9731.8644560.691.087100
2.56-2.645.090.8332.1943670.7920.928100
2.64-2.715.3020.6542.8842760.8750.72699.8
2.71-2.85.2650.5323.5541410.9070.59199.8
2.8-2.895.2210.4224.2740550.950.46999.9
2.89-2.995.1420.355.0738900.9590.3999.8
2.99-3.14.8960.2716.0737750.970.30399.9
3.1-3.235.1530.2237.6336040.980.24899.9
3.23-3.375.0410.1589.9734680.990.17799.6
3.37-3.545.1240.12112.5433220.9930.13599.8
3.54-3.735.3090.09215.3431260.9960.10299.9
3.73-3.955.1850.07318.2429930.9970.08199.8
3.95-4.235.060.0620.7827940.9980.06799.9
4.23-4.564.6910.05322.3326360.9980.05999.1
4.56-55.020.04623.8323930.9990.05299.9
5-5.594.9590.04823.2321930.9980.05399.7
5.59-6.465.1480.0523.1319500.9990.05599.9
6.46-7.914.9120.04325.9216230.9980.04899.7
7.91-11.184.7170.03431.5912870.9990.03999.3
11.18-48.6684.9840.03533.867070.9990.03997.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MCQ

6mcq


Resolution: 2.5→48.668 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2333 3053 5 %
Rwork0.1943 --
obs0.1962 61014 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 203.9 Å2 / Biso mean: 74.9598 Å2 / Biso min: 27.93 Å2
Refinement stepCycle: final / Resolution: 2.5→48.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10943 0 275 109 11327
Biso mean--90.56 55.95 -
Num. residues----1391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3036X-RAY DIFFRACTION7.036TORSIONAL
12C3036X-RAY DIFFRACTION7.036TORSIONAL
21B1060X-RAY DIFFRACTION7.036TORSIONAL
22D1060X-RAY DIFFRACTION7.036TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5390.35571350.315825742709100
2.539-2.58070.31321390.289226412780100
2.5807-2.62510.31271390.277626262765100
2.6251-2.67290.32571400.261926582798100
2.6729-2.72430.2911350.22925592694100
2.7243-2.77990.24831400.225526662806100
2.7799-2.84030.27761360.226925902726100
2.8403-2.90640.2881390.241826372776100
2.9064-2.97910.25541400.229726572797100
2.9791-3.05960.29611370.240226052742100
3.0596-3.14960.3021390.233326402779100
3.1496-3.25130.28361400.225326442784100
3.2513-3.36740.25971380.217726322770100
3.3674-3.50220.25241370.20226092746100
3.5022-3.66160.24511400.201626482788100
3.6616-3.85450.25641390.186226462785100
3.8545-4.09590.21961400.167826472787100
4.0959-4.4120.18791370.15342605274299
4.412-4.85560.19871410.148626892830100
4.8556-5.55740.20131390.169726302769100
5.5574-6.99840.23011400.200626632803100
6.9984-48.67760.17131430.17092695283899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.52470.14890.59094.73980.58083.6153-0.25190.2468-0.0337-0.13250.2865-0.4359-0.22360.3073-0.02150.3432-0.11380.04390.315-0.03530.2594100.623555.7753.3828
23.8623-0.25811.45671.3736-0.06784.4008-0.15550.21970.2153-0.1364-0.00640.0979-0.3699-0.08810.1830.3869-0.05160.01710.2974-0.01830.391685.567752.967249.8009
31.7434-0.141-0.08942.50220.58031.4322-0.0011-0.13420.08660.06840.03830.3789-0.108-0.1832-0.07350.3104-0.01230.03310.28330.02470.357955.803954.086566.7063
43.23271.17-0.97482.83950.68792.2248-0.1830.1572-0.2942-0.12120.17550.01680.1803-0.0556-0.01510.3546-0.04350.0090.2510.02790.44263.891524.999760.9906
55.3023-3.3637-0.48522.6547-0.9557.1571-0.0254-0.65010.1088-0.08160.76050.8111-0.2753-0.418-0.68040.56030.08140.05650.80140.07591.005538.651261.488521.9113
66.46860.09311.10273.3816-0.2984.93480.0626-0.98760.0629-0.00270.05550.2095-0.3741-0.5615-0.13620.42260.07970.04720.66170.01210.518352.71958.163624.2341
73.7597-0.9291-0.7061.2564-0.06321.46180.10690.45390.4594-0.0837-0.0069-0.3297-0.25750.0537-0.1380.5231-0.00510.02830.5082-0.00330.522582.72359.9228.2533
85.6822-0.9065-1.85923.5222-0.84924.0045-0.4051-0.0534-0.7163-0.02030.29390.16280.3653-0.06360.10980.54520.01430.09110.4708-0.0620.813675.780231.0614.2733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 104 )A10 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 258 )A105 - 258
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 529 )A259 - 529
4X-RAY DIFFRACTION4chain 'B'B31 - 213
5X-RAY DIFFRACTION5chain 'C' and (resid 11 through 104 )C11 - 104
6X-RAY DIFFRACTION6chain 'C' and (resid 105 through 253 )C105 - 253
7X-RAY DIFFRACTION7chain 'C' and (resid 254 through 529 )C254 - 529
8X-RAY DIFFRACTION8chain 'D'D32 - 212

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