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- PDB-3w1k: Crystal structure of the selenocysteine synthase SelA and tRNASec... -

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Basic information

Entry
Database: PDB / ID: 3w1k
TitleCrystal structure of the selenocysteine synthase SelA and tRNASec complex
Components
  • L-seryl-tRNA(Sec) selenium transferase
  • selenocysteine tRNA
KeywordsTRANSFERASE/RNA / protein-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
Function / homology
Function and homology information


L-seryl-tRNASec selenium transferase / L-seryl-tRNA(Sec) selenium transferase activity / conversion of seryl-tRNAsec to selenocys-tRNAsec / selenocysteine incorporation / identical protein binding / cytoplasm
Similarity search - Function
L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / RNA / RNA (> 10) / L-seryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Thermoanaerobacter tengcongensis MB4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.5 Å
AuthorsItoh, Y. / Sekine, S. / Yokoyama, S.
CitationJournal: Science / Year: 2013
Title: Decameric SelA-tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation
Authors: Itoh, Y. / Brocker, M.J. / Sekine, S. / Hammond, G. / Suetsugu, S. / Soll, D. / Yokoyama, S.
History
DepositionNov 15, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
C: L-seryl-tRNA(Sec) selenium transferase
D: L-seryl-tRNA(Sec) selenium transferase
E: L-seryl-tRNA(Sec) selenium transferase
F: selenocysteine tRNA
G: selenocysteine tRNA
H: selenocysteine tRNA
I: selenocysteine tRNA
J: selenocysteine tRNA


Theoretical massNumber of molelcules
Total (without water)407,08610
Polymers407,08610
Non-polymers00
Water00
1
A: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
C: L-seryl-tRNA(Sec) selenium transferase
D: L-seryl-tRNA(Sec) selenium transferase
E: L-seryl-tRNA(Sec) selenium transferase
F: selenocysteine tRNA
G: selenocysteine tRNA
H: selenocysteine tRNA
I: selenocysteine tRNA
J: selenocysteine tRNA

A: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
C: L-seryl-tRNA(Sec) selenium transferase
D: L-seryl-tRNA(Sec) selenium transferase
E: L-seryl-tRNA(Sec) selenium transferase
F: selenocysteine tRNA
G: selenocysteine tRNA
H: selenocysteine tRNA
I: selenocysteine tRNA
J: selenocysteine tRNA


Theoretical massNumber of molelcules
Total (without water)814,17220
Polymers814,17220
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)148.553, 355.972, 165.495
Angle α, β, γ (deg.)90.00, 115.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-seryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase


Mass: 50925.160 Da / Num. of mol.: 5 / Mutation: K19A, K21A, K46A, K48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: selA / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O67140, L-seryl-tRNASec selenium transferase
#2: RNA chain
selenocysteine tRNA


Mass: 30492.035 Da / Num. of mol.: 5 / Source method: obtained synthetically
Details: The tRNASec from Thermoanaerobacter tengcongensis MB4 was prepared by in vitro transcription with T7 RNA polymerase.
Source: (synth.) Thermoanaerobacter tengcongensis MB4 (bacteria)
References: GenBank: 20671658

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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: 4.85 Å3/Da / Density % sol: 74.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% ethylene glycol, 95mM NaNO3, 20mM Tris-HCl, 0.2M NaCl, 10mM MgCl2, 3mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2009 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.5→50 Å / Num. all: 9956 / Num. obs: 9777 / % possible obs: 98.2 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Biso Wilson estimate: 250 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 16.3
Reflection shellResolution: 7.5→7.77 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2.04 / Num. unique all: 990 / Rsym value: 0.712 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W1H

3w1h


Resolution: 7.5→49.94 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 7615012.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 475 4.9 %RANDOM
Rwork0.194 ---
obs0.194 9754 98.2 %-
all-9933 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 314.482 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 525.5 Å2
Baniso -1Baniso -2Baniso -3
1-185.25 Å2-0 Å268.26 Å2
2---71.44 Å20 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.12 Å0.8 Å
Luzzati d res low-20 Å
Luzzati sigma a1.78 Å1.08 Å
Refinement stepCycle: LAST / Resolution: 7.5→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17875 9785 0 0 27660
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it9.291.5
X-RAY DIFFRACTIONc_mcangle_it15.732
X-RAY DIFFRACTIONc_scbond_it20.942
X-RAY DIFFRACTIONc_scangle_it32.382.5
LS refinement shellResolution: 7.5→7.97 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 83 5.2 %
Rwork0.349 1509 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_add_LLP.paramprotein_add_LLP.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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