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- PDB-5x6b: Crystal structure of SepCysE-SepCysS in complex with tRNACys from... -

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Basic information

Entry
Database: PDB / ID: 5x6b
TitleCrystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus jannaschii
Components
  • O-phospho-L-seryl-tRNA:Cys-tRNA synthase
  • Uncharacterized protein MJ1481
  • tRNACys
KeywordsRNA BINDING PROTEIN/RNA / SepCysE / multidomain protein / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


O-phospho-L-seryl-tRNA:Cys-tRNA synthase / Sep-tRNA:Cys-tRNA synthase activity / translation
Similarity search - Function
Uncharacterised protein MJ1481, archaea / Uncharacterized protein conserved in archaea (DUF2100) / O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Uncharacterised protein MJ1481, archaea / Uncharacterized protein conserved in archaea (DUF2100) / O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Uncharacterized protein MJ1481 / O-phospho-L-seryl-tRNA:Cys-tRNA synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
Methanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsChen, M. / Kato, K. / Yao, M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for tRNA-dependent cysteine biosynthesis
Authors: Chen, M. / Kato, K. / Kubo, Y. / Tanaka, Y. / Liu, Y. / Long, F. / Whitman, W.B. / Lill, P. / Gatsogiannis, C. / Raunser, S. / Shimizu, N. / Shinoda, A. / Nakamura, A. / Tanaka, I. / Yao, M.
History
DepositionFeb 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
J: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
E: Uncharacterized protein MJ1481
F: Uncharacterized protein MJ1481
P: tRNACys


Theoretical massNumber of molelcules
Total (without water)169,8765
Polymers169,8765
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19440 Å2
ΔGint-118 kcal/mol
Surface area50460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.252, 107.252, 551.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein O-phospho-L-seryl-tRNA:Cys-tRNA synthase / / Sep-tRNA:Cys-tRNA synthase / SepCysS


Mass: 47538.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MJ1678 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59072*PLUS
#2: Protein Uncharacterized protein MJ1481


Mass: 25334.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1481 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58876
#3: RNA chain tRNACys


Mass: 24129.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE ENTITY SEQUENCE OF THE CHAIN I OR J MAPPED TO GB AAB99700.1 RESIDUE 1 TO 396.

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5 / Details: 0.1M MES pH 5.0, 2.4M Ammonium Sulfate / PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CCD / Date: Oct 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.596→48.221 Å / Num. obs: 59370 / % possible obs: 99.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 18.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKR, 1B23

3wkr

1b23


Resolution: 2.596→48.221 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.94
RfactorNum. reflection% reflection
Rfree0.2614 2927 4.93 %
Rwork0.2245 --
obs0.2263 59360 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.596→48.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7977 1599 0 45 9621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059911
X-RAY DIFFRACTIONf_angle_d1.09213696
X-RAY DIFFRACTIONf_dihedral_angle_d14.7644029
X-RAY DIFFRACTIONf_chiral_restr0.0621563
X-RAY DIFFRACTIONf_plane_restr0.0051458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5962-2.63880.40841260.34292496X-RAY DIFFRACTION96
2.6388-2.68430.33361500.31092668X-RAY DIFFRACTION100
2.6843-2.73310.35131170.2962615X-RAY DIFFRACTION100
2.7331-2.78560.3321420.28332627X-RAY DIFFRACTION100
2.7856-2.84250.33161350.27962654X-RAY DIFFRACTION100
2.8425-2.90430.31551330.26732651X-RAY DIFFRACTION100
2.9043-2.97180.33281410.26522617X-RAY DIFFRACTION100
2.9718-3.04610.33891380.25342650X-RAY DIFFRACTION100
3.0461-3.12850.28441310.2542653X-RAY DIFFRACTION100
3.1285-3.22050.28431420.26472654X-RAY DIFFRACTION100
3.2205-3.32440.29981280.25892672X-RAY DIFFRACTION100
3.3244-3.44320.28061390.25462682X-RAY DIFFRACTION100
3.4432-3.58110.29341470.23492673X-RAY DIFFRACTION100
3.5811-3.7440.26441350.21662647X-RAY DIFFRACTION100
3.744-3.94130.251490.20652697X-RAY DIFFRACTION100
3.9413-4.18810.24961530.19922680X-RAY DIFFRACTION100
4.1881-4.51120.21671550.1982716X-RAY DIFFRACTION100
4.5112-4.96480.24281450.19072726X-RAY DIFFRACTION100
4.9648-5.68220.20671310.21062785X-RAY DIFFRACTION100
5.6822-7.15530.25681410.21952834X-RAY DIFFRACTION100
7.1553-48.22980.22751490.20273036X-RAY DIFFRACTION99

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