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- PDB-3am1: Crystal structure of O-Phosphoseryl-tRNA kinase complexed with an... -

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Basic information

Entry
Database: PDB / ID: 3am1
TitleCrystal structure of O-Phosphoseryl-tRNA kinase complexed with anticodon-stem/loop truncated tRNA(Sec)
Components
  • ASL-truncated tRNA
  • L-seryl-tRNA(Sec) kinase
KeywordsTRANSFERASE/RNA / kinase / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / L-seryl-tRNA(Sec) kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAraiso, Y. / Ishitani, R. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec)
Authors: Sherrer, R.L. / Araiso, Y. / Aldag, C. / Ishitani, R. / Ho, J.M.L. / Soll, D. / Nureki, O.
History
DepositionAug 11, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 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 / 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 / _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: ASL-truncated tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7324
Polymers57,2012
Non-polymers5312
Water1267
1
A: L-seryl-tRNA(Sec) kinase
B: ASL-truncated tRNA
hetero molecules

A: L-seryl-tRNA(Sec) kinase
B: ASL-truncated tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4648
Polymers114,4014
Non-polymers1,0634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area7100 Å2
ΔGint-48 kcal/mol
Surface area48010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.749, 46.749, 459.712
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

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


Mass: 31009.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: pstK, MJ1538 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q58933, O-phosphoseryl-tRNASec kinase
#2: RNA chain ASL-truncated tRNA


Mass: 26191.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized RNA
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.54 Å3/Da / Density % sol: 51.48 % / Mosaicity: 0.21 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100mM phosphate buffer (pH 6.2), 0.2M NaCl, 41% PEG 200, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22946 / % possible obs: 97.6 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.111 / Χ2: 1.561 / Net I/σ(I): 25.886
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.4440.3929350.778179.4
2.44-2.494.70.4189720.857185.3
2.49-2.535.70.39710700.842194.2
2.53-2.596.40.39511470.817196.8
2.59-2.647.80.40911280.846199.3
2.64-2.79.20.37811520.864199.8
2.7-2.7710.90.36811560.887199.8
2.77-2.8512.40.33811180.967199.8
2.85-2.9313.20.28912311.11199.9
2.93-3.0215.20.24811091.309199.9
3.02-3.1316.10.20911901.385199.9
3.13-3.26170.17711341.587199.9
3.26-3.4117.50.16411861.703199.9
3.41-3.58190.15211751.664199.7
3.58-3.8119.20.12211521.5581100
3.81-4.119.90.12111901.7671100
4.1-4.5220.60.11911872.056199.9
4.52-5.1720.50.13612212.552199.9
5.17-6.5120.40.11712142.064199.8
6.51-5019.30.05412791.443197.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A4N

3a4n


Resolution: 2.4→34.463 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6875 / SU ML: 0.41 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 1145 5.01 %Random
Rwork0.2293 ---
obs0.2324 22838 97.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.186 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 244.14 Å2 / Biso mean: 80.578 Å2 / Biso min: 29.58 Å2
Baniso -1Baniso -2Baniso -3
1-7.7234 Å2-0 Å2-0 Å2
2--7.7234 Å20 Å2
3----15.4468 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 1734 32 7 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063876
X-RAY DIFFRACTIONf_angle_d1.5365651
X-RAY DIFFRACTIONf_chiral_restr0.077710
X-RAY DIFFRACTIONf_plane_restr0.005406
X-RAY DIFFRACTIONf_dihedral_angle_d20.2761676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4002-2.50940.50781250.44572289241484
2.5094-2.64170.43811390.3792685282497
2.6417-2.80710.39571460.326527322878100
2.8071-3.02370.35141410.275627362877100
3.0237-3.32780.27291440.227427922936100
3.3278-3.80880.27621420.192127282870100
3.8088-4.79660.23351530.167628212974100
4.7966-34.46680.25591550.205329103065100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6809-0.0253-0.24960.04370.14160.4774-0.0070.5590.1521-0.25370.149-0.33290.2717-0.1335-0.0430.671-0.15350.0331-0.02740.08890.38262.003628.580761.0978
20.3932-0.0815-0.13730.0388-0.0050.11580.05750.0073-0.3218-0.5583-0.1613-0.3030.0983-0.0530.0590.74520.07040.0218-0.36240.11160.36956.6939-15.375418.5734
30.716-0.14720.10271.07240.27710.18780.01330.1570.10370.051-0.12910.1804-0.3329-0.01950.03920.5235-0.00160.06550.3309-0.01540.25458.39886.684826.327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 3:177A3 - 177
2X-RAY DIFFRACTION2chain A and resid 189:252A189 - 252
3X-RAY DIFFRACTION3chain BB1 - 81

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