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- PDB-9fmo: Crystal structure of C. merolae LAMMER-like dual specificity kina... -

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Basic information

Entry
Database: PDB / ID: 9fmo
TitleCrystal structure of C. merolae LAMMER-like dual specificity kinase (CmLIK) kinase domain
ComponentsLAMMER-like dual specificity kinase
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
LAMMER-like dual specificity kinase
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.487 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,0153
Polymers42,8871
Non-polymers1272
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-21 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.522, 70.393, 88.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M1UWB5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 298 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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 26, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.487→50 Å / Num. obs: 14748 / % possible obs: 99 % / Redundancy: 7.4 % / Biso Wilson estimate: 54.48 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.39
Reflection shellResolution: 2.49→2.64 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2323 / CC1/2: 0.327

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.487→37.38 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 737 5.01 %
Rwork0.2299 --
obs0.2318 14723 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.487→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2880 0 5 13 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032982
X-RAY DIFFRACTIONf_angle_d0.5724043
X-RAY DIFFRACTIONf_dihedral_angle_d5.552506
X-RAY DIFFRACTIONf_chiral_restr0.045443
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.487-2.67890.35861450.32112750X-RAY DIFFRACTION99
2.6789-2.94830.40321450.30562752X-RAY DIFFRACTION99
2.9483-3.37470.32951450.27482751X-RAY DIFFRACTION99
3.3747-4.25090.25221490.20972831X-RAY DIFFRACTION100
4.2509-37.380.21061530.1952902X-RAY DIFFRACTION98

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