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- PDB-3a4m: Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase -

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Basic information

Entry
Database: PDB / ID: 3a4m
TitleCrystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase
ComponentsL-seryl-tRNA(Sec) kinase
KeywordsTRANSFERASE / P-LOOP MOTIF / WALKER A MOTIF / ATP BINDING MOTIF / ATP-binding / Kinase / Nucleotide-binding
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
ADENOSINE-5'-DIPHOSPHATE / IODIDE ION / L-seryl-tRNA(Sec) kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.792 Å
AuthorsAraiso, Y. / Ishitani, R. / Soll, D. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of a tRNA-dependent kinase essential for selenocysteine decoding
Authors: Araiso, Y. / Sherrer, R.L. / Ishitani, R. / Ho, J.M.L. / Soll, D. / Nureki, O.
History
DepositionJul 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,42312
Polymers62,0182
Non-polymers1,40510
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-30 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.156, 74.524, 64.817
Angle α, β, γ (deg.)90.00, 113.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 31009.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: K-12 / Gene: MJ1538 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q58933, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 5 types, 275 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10mM HEPES-NaOH, 250mM KI and 21% PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONSPring-8 BL41XU20.9791, 0.9794, 0.9642
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 15, 2008
ADSC QUANTUM 3152CCDOct 19, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97941
40.96421
ReflectionResolution: 1.79→50 Å / Num. obs: 47081 / Biso Wilson estimate: 22.67 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.792→46.498 Å / FOM work R set: 0.837 / SU ML: 0.29 / σ(F): 0.03 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 2351 5 %
Rwork0.2092 --
obs0.2114 47054 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.894 Å2 / ksol: 0.403 e/Å3
Displacement parametersBiso mean: 28.458 Å2
Baniso -1Baniso -2Baniso -3
1--4.863 Å2-0 Å22.822 Å2
2--2.43 Å2-0 Å2
3---2.433 Å2
Refinement stepCycle: LAST / Resolution: 1.792→46.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 74 265 4320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0234115
X-RAY DIFFRACTIONf_angle_d1.9265512
X-RAY DIFFRACTIONf_dihedral_angle_d20.0691622
X-RAY DIFFRACTIONf_chiral_restr0.139614
X-RAY DIFFRACTIONf_plane_restr0.009665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7917-1.82830.28611280.24522272X-RAY DIFFRACTION85
1.8283-1.86810.30871290.23962564X-RAY DIFFRACTION96
1.8681-1.91150.27051300.22172602X-RAY DIFFRACTION98
1.9115-1.95930.26851390.20162603X-RAY DIFFRACTION99
1.9593-2.01230.24871540.19192669X-RAY DIFFRACTION99
2.0123-2.07150.24571270.18642632X-RAY DIFFRACTION99
2.0715-2.13840.24621510.18962633X-RAY DIFFRACTION100
2.1384-2.21480.25611410.19342627X-RAY DIFFRACTION99
2.2148-2.30350.27171310.19882687X-RAY DIFFRACTION99
2.3035-2.40830.30051450.20082658X-RAY DIFFRACTION100
2.4083-2.53530.24971360.20342659X-RAY DIFFRACTION100
2.5353-2.69410.26411420.21332635X-RAY DIFFRACTION100
2.6941-2.90210.28071340.21082676X-RAY DIFFRACTION100
2.9021-3.19410.27571420.21862684X-RAY DIFFRACTION100
3.1941-3.65610.2151410.19852688X-RAY DIFFRACTION100
3.6561-4.60570.21091320.1812691X-RAY DIFFRACTION100
4.6057-46.51380.23091490.2292723X-RAY DIFFRACTION99

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