5LNM

Crystal structure of D1050E mutant of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana

> Summary

Summary for 5LNM

DescriptorHistidine kinase CKI1 (2 entities in total)
Functional Keywordsreceiver domain, mutant, histidine kinase cki1, (alpha/beta)5 fold, transferase
Biological sourceArabidopsis thaliana (Mouse-ear cress)
Cellular locationCell membrane ; Multi-pass membrane protein  O22267
Total number of polymer chains1
Total molecular weight23239.9
Authors
Primary citation
Otrusinova, O.,Demo, G.,Padrta, P.,Jasenakova, Z.,Pekarova, B.,Gelova, Z.,Szmitkowska, A.,Kaderavek, P.,Jansen, S.,Zachrdla, M.,Klumpler, T.,Marek, J.,Hritz, J.,Janda, L.,Iwai, H.,Wimmerova, M.,Hejatko, J.,Zidek, L.
Conformational dynamics as a key factor of signaling mediated by the receiver domain of sensor histidine kinase from Arabidopsis thaliana.
J. Biol. Chem., 2017
PubMed: 28860196 (PDB entries with the same primary citation)
DOI: 10.1074/jbc.M117.790212
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.95 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.23980.7%4.6%2.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5lnm
no rotation
Molmil generated image of 5lnm
rotated about x axis by 90°
Molmil generated image of 5lnm
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AHistidine kinase CKI1polymer20623239.91
UniProt (O22267)
Pfam (PF00072)
Arabidopsis thaliana (Mouse-ear cress)Protein CYTOKININ-INDEPENDENT 1
waterwater18.094

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight23239.9
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight23239.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.95 Å)

Cell axes54.33798.72879.897
Cell angles90.0090.0090.00
SpacegroupC 2 2 21
Resolution limits42.37 - 1.95
the highest resolution shell value2.001 - 1.950
R-factor0.20848
R-work0.20718
the highest resolution shell value0.532
R-free0.23381
the highest resolution shell value0.505
RMSD bond length0.019
RMSD bond angle2.037

Data Collection Statistics

Resolution limits47.60 - 1.95
the highest resolution shell value -
Number of reflections15893
Rmerge_l_obs0.117
the highest resolution shell value0.665
Completeness99.2
Redundancy5.7
the highest resolution shell value4

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP5.05290.15

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI142Helical. {ECO:0000255}.
ChainResidueDetails
ANA*
ANA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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