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- PDB-2z67: Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium t... -

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Basic information

Entry
Database: PDB / ID: 2z67
TitleCrystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS)
ComponentsO-phosphoseryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / selenocysteine biosynthesis / seven-stranded bete-strand / PYRIDOXAL-5'-PHOSPHATE / Protein biosynthesis / Pyridoxal phosphate / Selenium
Function / homology
Function and homology information


selenotransferase activity / : / O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase / tRNA binding / translation
Similarity search - Function
O-phosphoseryl-tRNA(Sec) selenium transferase / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsAraiso, Y. / Ishitani, R. / Pailouer, S. / Oshikane, H. / Domae, N. / Soll, D. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation.
Authors: Araiso, Y. / Palioura, S. / Ishitani, R. / Sherrer, R.L. / O'Donoghue, P. / Yuan, J. / Oshikane, H. / Domae, N. / Defranco, J. / Soll, D. / Nureki, O.
History
DepositionJul 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,78110
Polymers204,6004
Non-polymers1,1816
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28240 Å2
ΔGint-194 kcal/mol
Surface area56510 Å2
MethodPISA
2
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8915
Polymers102,3002
Non-polymers5903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-64 kcal/mol
Surface area33200 Å2
MethodPISA
3
A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8915
Polymers102,3002
Non-polymers5903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-61 kcal/mol
Surface area33090 Å2
MethodPISA
4
A: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7944
Polymers102,3002
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-37 kcal/mol
Surface area37230 Å2
MethodPISA
5
B: O-phosphoseryl-tRNA(Sec) selenium transferase
C: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9876
Polymers102,3002
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-61 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.745, 108.143, 110.390
Angle α, β, γ (deg.)90.00, 96.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
O-phosphoseryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNASec / synthase / Sep-tRNA:Sec-tRNA ...Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNASec / synthase / Sep-tRNA:Sec-tRNA synthase / SepSecS


Mass: 51150.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: S2 / Gene: spcS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)codon plus / References: UniProt: Q6LZM9, EC: 2.9.1.-
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791, 0.9793, 0.9820, 0.9770
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2006 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.9821
40.9771
ReflectionResolution: 2.5→50 Å / Num. all: 59938 / Num. obs: 59938 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.135 / Net I/σ(I): 17
Reflection shellResolution: 2.5→50 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2627 / Rsym value: 0.258 / % possible all: 86.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2595839.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3020 5 %RANDOM
Rwork0.208 ---
obs0.208 59930 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.9936 Å2 / ksol: 0.311972 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-6.52 Å2
2--1.65 Å20 Å2
3----1.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13548 0 70 146 13764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 477 5.1 %
Rwork0.262 8805 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2PLP.paramPLP.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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