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

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Basic information

Entry
Database: PDB / ID: 9fmq
TitleCrystal structure of C. merolae LAMMER-like dual specificity kinase (CmLIK) hairpin mutant 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
ACETATE ION / LAMMER-like dual specificity kinase
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,49712
Polymers43,8421
Non-polymers65511
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint18 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.720, 68.670, 84.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LAMMER-like dual specificity kinase


Mass: 43842.457 Da / Num. of mol.: 1
Mutation: 610PSSYYPNRQITEHVQ624 > 610KSDYTEAYNPKMKRDERTIVNPD632
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.25 M calcium acetate, 14 % (w/v) PEG3350, 20 % (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 20, 2022
RadiationMonochromator: Si-111 and Si-113 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 37481 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 19.94
Reflection shellResolution: 1.77→1.88 Å / Num. unique obs: 5958 / CC1/2: 0.544

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→42.36 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1874 5 %
Rwork0.1919 --
obs0.1939 37478 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 41 83 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113002
X-RAY DIFFRACTIONf_angle_d1.1154055
X-RAY DIFFRACTIONf_dihedral_angle_d14.0331139
X-RAY DIFFRACTIONf_chiral_restr0.069445
X-RAY DIFFRACTIONf_plane_restr0.012528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.33391420.31232700X-RAY DIFFRACTION100
1.82-1.870.28011410.27462693X-RAY DIFFRACTION100
1.87-1.930.29071430.26962707X-RAY DIFFRACTION100
1.93-20.28891410.23012676X-RAY DIFFRACTION100
2-2.080.27691430.20822727X-RAY DIFFRACTION100
2.08-2.180.28551430.20472710X-RAY DIFFRACTION100
2.18-2.290.21641430.19792713X-RAY DIFFRACTION100
2.29-2.430.25041430.20362722X-RAY DIFFRACTION100
2.43-2.620.22651440.19612743X-RAY DIFFRACTION100
2.62-2.890.24171440.20962734X-RAY DIFFRACTION100
2.89-3.30.27961450.21182760X-RAY DIFFRACTION100
3.3-4.160.21831470.17722791X-RAY DIFFRACTION100
4.16-42.360.19421550.17112928X-RAY DIFFRACTION100
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)
11.3715-1.26831.50762.7293-0.26074.0767-0.26780.14760.26950.3253-0.036-0.5219-0.59420.59190.21730.4217-0.0842-0.06010.40680.05830.46064.2093-11.026221.511
21.8660.4499-0.1023.3755-0.03843.413-0.10260.2177-0.0683-0.09910.03860.08850.03170.17930.07250.24730.0262-0.03130.3238-0.01630.328-8.8931-6.7053-1.9951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 453 through 572 )
2X-RAY DIFFRACTION2chain 'A' and (resid 573 through 816 )

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