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- PDB-3adb: Crystal structure of O-phosphoseryl-tRNA kinase complexed with se... -

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Basic information

Entry
Database: PDB / ID: 3adb
TitleCrystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 1)
Components
  • L-seryl-tRNA(Sec) kinase
  • selenocysteine tRNA
KeywordsTRANSFERASE/RNA / Protein-RNA complex / tRNA / ATP-binding / Kinase / Nucleotide-binding / Transferase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


O-phosphoseryl-tRNASec kinase / L-seryl-tRNA(Sec) kinase activity / conversion of seryl-tRNAsec to selenocys-tRNAsec / tRNA wobble uridine modification / phosphorylation / ATP binding
Similarity search - Function
Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #40 / L-seryl-tRNA(Sec) kinase, archaea / Protein KTI12/L-seryl-tRNA(Sec) kinase / Chromatin associated protein KTI12 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #40 / L-seryl-tRNA(Sec) kinase, archaea / Protein KTI12/L-seryl-tRNA(Sec) kinase / Chromatin associated protein KTI12 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / RNA / RNA (> 10) / L-seryl-tRNA(Sec) kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Methanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsItoh, Y. / Chiba, S. / Sekine, S. / Yokoyama, S.
CitationJournal: Mol.Cell / Year: 2010
Title: Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine
Authors: Chiba, S. / Itoh, Y. / Sekine, S. / Yokoyama, S.
History
DepositionJan 18, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-seryl-tRNA(Sec) kinase
B: L-seryl-tRNA(Sec) kinase
C: selenocysteine tRNA
D: selenocysteine tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4487
Polymers121,8234
Non-polymers6253
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-60 kcal/mol
Surface area55960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.196, 260.923, 45.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein L-seryl-tRNA(Sec) kinase / O-phosphoseryl-tRNA(Sec) kinase / PSTK


Mass: 31196.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ1538 / Plasmid: pCold II / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: Q58933, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: RNA chain selenocysteine tRNA


Mass: 29714.688 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: tRNASec was prepared by in vitro transcription with T7 RNA polymerase.
Source: (synth.) Methanopyrus kandleri (archaea)

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Non-polymers , 4 types, 162 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRNA USES NON-SEQUENTIAL NUMBERING. NUMBER 17 IS SIMPLY SKIPPED IN BOTH RNA.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 14.5% PEG 3350, 40mM sodium citrate-HCl (pH 5.2), 260mM ammonium tartrate, 5.0mM magnesium chloride, 1.0mM AMPPNP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONPhoton Factory AR-NW12A20.97904, 0.97931, 0.96408
Detector
TypeIDDetectorDateDetails
RAYONIX MX225HE1CCDMay 26, 2009monochromator
ADSC QUANTUM 2102CCDApr 26, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SiMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979041
30.979311
40.964081
ReflectionResolution: 2.8→50 Å / Num. all: 28439 / Num. obs: 28411 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 88.8 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 14.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.01 / Num. unique all: 2779 / Rsym value: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
autoSHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→40.84 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2027121.55 / 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
Rfree0.269 1421 5.1 %RANDOM
Rwork0.228 ---
obs0.23 28071 99.9 %-
all-28112 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 3.13239 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--16.26 Å20 Å2
3----15.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 3936 37 159 8306
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.831.5
X-RAY DIFFRACTIONc_mcangle_it4.022
X-RAY DIFFRACTIONc_scbond_it3.612
X-RAY DIFFRACTIONc_scangle_it4.992.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 228 5 %
Rwork0.349 4343 -
obs-4571 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ANP.paramANP.top

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