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- PDB-9fmp: Crystal structure of phosphorylated C. merolae LAMMER-like dual s... -

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Basic information

Entry
Database: PDB / ID: 9fmp
TitleCrystal structure of phosphorylated C. merolae LAMMER-like dual specificity kinase (CmLIK) kinase domain in complex with adenosine
Components(LAMMER-like dual specificity kinase) x 2
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE
Function / homology
Function and homology information


protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE / LAMMER-like dual specificity kinase
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsDimos-Roehl, B. / Haltenhof, T. / Kotte, A. / Heyd, F. / Loll, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal structure of C. merolae LAMMER-like dual specificity kinase CmLIK kinase domain
Authors: Dimos-Roehl, B. / Haltenhof, T. / Kotte, A. / Heyd, F. / Loll, B.
History
DepositionJun 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAMMER-like dual specificity kinase
B: LAMMER-like dual specificity kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06531
Polymers85,8552
Non-polymers2,21029
Water1,65792
1
A: LAMMER-like dual specificity kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,08617
Polymers42,8871
Non-polymers1,19816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LAMMER-like dual specificity kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,97914
Polymers42,9671
Non-polymers1,01213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.126, 100.892, 109.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein LAMMER-like dual specificity kinase


Mass: 42887.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Gene: CYME_CMR245C / Plasmid: pGex-6P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1UWB5
#2: Protein LAMMER-like dual specificity kinase


Mass: 42967.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Gene: CYME_CMR245C / Plasmid: pGex-6P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1UWB5
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.0, 20 % (v/v) ethanol, 30 % (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 25, 2020
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 22375 / % possible obs: 99.2 % / Redundancy: 13.2 % / Biso Wilson estimate: 40.67 Å2 / CC1/2: 0.976 / Net I/σ(I): 5.24
Reflection shellResolution: 2.69→2.85 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 3593 / CC1/2: 0.476

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→48.18 Å / SU ML: 0.363 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2678 1119 5 %
Rwork0.2032 21251 -
obs0.2064 22370 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.13 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5789 0 146 92 6027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286070
X-RAY DIFFRACTIONf_angle_d0.56648185
X-RAY DIFFRACTIONf_chiral_restr0.0441896
X-RAY DIFFRACTIONf_plane_restr0.00541047
X-RAY DIFFRACTIONf_dihedral_angle_d14.35172261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.810.3361310.2652496X-RAY DIFFRACTION93.99
2.81-2.960.29351390.2562627X-RAY DIFFRACTION99.93
2.96-3.150.30871380.2522622X-RAY DIFFRACTION100
3.15-3.390.36011390.23422650X-RAY DIFFRACTION99.96
3.39-3.730.31141400.20582663X-RAY DIFFRACTION100
3.73-4.270.24281400.18292664X-RAY DIFFRACTION100
4.27-5.380.22251430.16322707X-RAY DIFFRACTION100
5.38-48.180.21041490.18392822X-RAY DIFFRACTION99.76
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)
10.9294808868460.460858707634-0.2025625266560.460828887249-0.198489335390.08435016484530.002071810586370.0318574980867-0.231434138290.0679694543861-0.104206669354-0.1366373486160.02248445835920.085087234205-0.0002884317157360.253789937033-0.0167251447469-0.01033603400580.2161556500540.004338113661290.17036570963423.5398833691-23.8019903887-3.03871644366
20.1130967271810.2052682049030.001588115786070.375893951135-0.05072993767360.857911511248-0.01237182529340.00593872616920.0110328910924-0.0761666032656-0.0647160874070.06643658929060.005792778006830.0331953065594-5.92622158726E-50.209418652182-0.003916837286520.0009802249725850.1578455833610.02265208531720.23476906789829.8088844594-2.7576581022-14.6238807745
30.1610893505070.068177069004-0.0358624537470.1708711258320.09039459656630.0849465748697-0.0220951554270.268896162036-0.003844891119410.1074136858280.08638601055980.12481875002-0.0371931222418-0.07393532044840.000454284350660.2707631262-0.001997015710760.0383866439160.3237615898310.0490415953570.25816123114711.4458442123-27.7177464252-60.9612987511
40.792511845187-0.176893560152-0.2424635198640.119278650643-0.116178527840.685669159109-0.0616298984332-0.0587457833048-0.044031837354-0.0445511092589-0.05265599206750.002564144190780.0800823369612-0.00355004837292-0.01089820880380.178639628628-0.02287176578960.01055987279640.1872905175110.001523778377210.19497301656410.4637534011-30.3758355162-34.6209768848
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 449 through 608 )AA449 - 6081 - 160
22chain 'A' and (resid 609 through 809 )AA609 - 809161 - 361
33chain 'B' and (resid 451 through 522 )BB451 - 5221 - 72
44chain 'B' and (resid 523 through 808 )BB523 - 80873 - 357

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