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

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Basic information

Entry
Database: PDB / ID: 3add
TitleCrystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 3)
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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / L-seryl-tRNA(Sec) kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Methanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)122,8848
Polymers121,8234
Non-polymers1,0614
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-58 kcal/mol
Surface area54750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.860, 258.896, 45.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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)
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 %
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

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 26, 2009 / Details: monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 43686 / Num. obs: 39929 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 19
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.56 / Num. unique all: 4253 / Rsym value: 0.553 / % possible all: 88

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ADB

3adb


Resolution: 2.4→40.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1720323.08 / 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
Rfree0.258 2035 5.1 %RANDOM
Rwork0.218 ---
obs0.22 39869 91.1 %-
all-43752 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4913 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 67.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å20 Å2
2--12.26 Å20 Å2
3----14.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 3772 64 160 8109
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.111.5
X-RAY DIFFRACTIONc_mcangle_it4.582
X-RAY DIFFRACTIONc_scbond_it4.182
X-RAY DIFFRACTIONc_scangle_it5.842.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 322 5.2 %
Rwork0.32 5823 -
obs-6145 85.8 %
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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