3W1K

Crystal structure of the selenocysteine synthase SelA and tRNASec complex

> Summary

Summary for 3W1K

Related3W1H 3W1I 3W1J
DescriptorL-seryl-tRNA(Sec) selenium transferase (E.C.2.9.1.1)/RNA
Functional Keywordsprotein-rna complex, homodecamer, pentamer of dimers, fold-type i pyridoxal 5'-phosphate (plp) dependent enzyme, non-canonical trna, l-seryl-trna(sec) selenium transferase, selenocysteine synthesis, selenium metabolism, transferase-rna complex, transferase/rna
Biological sourceAquifex aeolicus
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Cellular locationCytoplasm (By similarity) O67140
Total number of polymer chains10
Total molecular weight407099.94
Authors
Itoh, Y.,Sekine, S.,Yokoyama, S. (deposition date: 2012-11-15, release date: 2013-06-05)
Primary citation
Itoh, Y.,Brocker, M.J.,Sekine, S.,Hammond, G.,Suetsugu, S.,Soll, D.,Yokoyama, S.
Decameric SelA-tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation
Science, 340:75-78, 2013
PubMed: 23559248
DOI: 10.1126/science.1229521
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (7.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.245351.0%1.2%18.2%0.54MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3w1k
no rotation
Molmil generated image of 3w1k
rotated about x axis by 90°
Molmil generated image of 3w1k
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 3w1k
no rotation
Molmil generated image of 3w1k
rotated about x axis by 90°
Molmil generated image of 3w1k
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (3w1k.pdb1.gz [1.09 MB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, D, EL-seryl-tRNA(Sec) selenium transferasepolymer45250927.85
UniProt (O67140)
Pfam (PF03841)
Aquifex aeolicusSelenocysteine synthase, Sec synthase, Selenocysteinyl-tRNA(Sec) synthase
F, G, H, I, Jselenocysteine tRNApolymer9530492.25
GeneBank (20671658)
Thermoanaerobacter tengcongensis MB4

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains10
Total molecular weight407099.9
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight407099.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (7.5 Å)

Cell axes148.553355.972165.495
Cell angles90.00115.4190.00
SpacegroupC 1 2 1
Resolution limits49.94 - 7.50
the highest resolution shell value7.970 - 7.500
R-factor0.194
R-work0.19400
the highest resolution shell value0.349
R-free0.24000
the highest resolution shell value0.398
RMSD bond length0.007
RMSD bond angle1.200

Data Collection Statistics

Resolution limits50.00 - 7.50
the highest resolution shell value -
Number of reflections9777
Rmerge_l_obs0.102
the highest resolution shell value0.712
Completeness98.2
Redundancy3.6
the highest resolution shell value2.9
I/sigma(I)-1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7.5293

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
A0005737cellular_componentcytoplasm
A0004125molecular_functionL-seryl-tRNASec selenium transferase activity
A0001514biological_processselenocysteine incorporation
A0097056biological_processselenocysteinyl-tRNA(Sec) biosynthetic process
B0005737cellular_componentcytoplasm
B0004125molecular_functionL-seryl-tRNASec selenium transferase activity
B0001514biological_processselenocysteine incorporation
B0097056biological_processselenocysteinyl-tRNA(Sec) biosynthetic process
C0005737cellular_componentcytoplasm
C0004125molecular_functionL-seryl-tRNASec selenium transferase activity
C0001514biological_processselenocysteine incorporation
C0097056biological_processselenocysteinyl-tRNA(Sec) biosynthetic process
D0005737cellular_componentcytoplasm
D0004125molecular_functionL-seryl-tRNASec selenium transferase activity
D0001514biological_processselenocysteine incorporation
D0097056biological_processselenocysteinyl-tRNA(Sec) biosynthetic process
E0005737cellular_componentcytoplasm
E0004125molecular_functionL-seryl-tRNASec selenium transferase activity
E0001514biological_processselenocysteine incorporation
E0097056biological_processselenocysteinyl-tRNA(Sec) biosynthetic process
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Functional Information from PDB Data

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

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Functional Information from PROSITE/UniProt

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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

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Catalytic Information from CATRES

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> Sequence Neighbor

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