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- PDB-3wks: Crystal structure of the SepCysS-SepCysE N-terminal domain comple... -

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Basic information

Entry
Database: PDB / ID: 3wks
TitleCrystal structure of the SepCysS-SepCysE N-terminal domain complex from
Components
  • O-phospho-L-seryl-tRNA:Cys-tRNA synthase
  • Uncharacterized protein MJ1481
KeywordsTRANSFERASE / aminoacyl tRNA synthesis
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
Uncharacterized protein MJ1481 / O-phospho-L-seryl-tRNA:Cys-tRNA synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.029 Å
AuthorsNakazawa, Y. / Asano, N. / Nakamura, A. / Yao, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea.
Authors: Liu, Y. / Nakamura, A. / Nakazawa, Y. / Asano, N. / Ford, K.A. / Hohn, M.J. / Tanaka, I. / Yao, M. / Soll, D.
History
DepositionOct 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
B: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
C: Uncharacterized protein MJ1481
D: Uncharacterized protein MJ1481


Theoretical massNumber of molelcules
Total (without water)119,9424
Polymers119,9424
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint-97 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.073, 107.135, 110.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47424.461 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: MJ1678 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59072, O-phospho-L-seryl-tRNA:Cys-tRNA synthase
#2: Protein Uncharacterized protein MJ1481 / SepCysE


Mass: 12546.692 Da / Num. of mol.: 2 / Fragment: UNP residues 1-103
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Succinic acid, PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 15, 2012
RadiationMonochromator: Si (11 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.029→50 Å / Num. obs: 22584 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.33 % / Biso Wilson estimate: 54.09 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.178 / Net I/σ(I): 12.38
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.029-3.217.310.8062.91198.6
3.21-3.430.4663.37199.9
3.43-3.710.295.3199.9
3.71-4.060.1738.341100
4.06-4.530.11611.781100
4.53-5.230.09413.71100
5.23-6.380.10512.441100
6.38-8.950.06218.771100
8.95-500.0428.8199.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.029→49.197 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.74 / σ(F): 1.36 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 2003 8.87 %
Rwork0.1889 --
obs0.1935 22573 99.72 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.515 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.9992 Å2-0 Å2-0 Å2
2---9.9806 Å20 Å2
3----3.0186 Å2
Refinement stepCycle: LAST / Resolution: 3.029→49.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7032 0 0 23 7055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027171
X-RAY DIFFRACTIONf_angle_d0.659631
X-RAY DIFFRACTIONf_dihedral_angle_d12.9642749
X-RAY DIFFRACTIONf_chiral_restr0.0431041
X-RAY DIFFRACTIONf_plane_restr0.0031219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0288-3.10450.37871320.2886141397
3.1045-3.18850.33361460.28321446100
3.1885-3.28230.31491380.26141456100
3.2823-3.38820.35341400.23611441100
3.3882-3.50920.29651440.23771450100
3.5092-3.64970.26761400.20621461100
3.6497-3.81580.23731460.18251451100
3.8158-4.01680.23321430.17161453100
4.0168-4.26840.18911450.16281470100
4.2684-4.59770.18721430.14561461100
4.5977-5.060.21021410.15451487100
5.06-5.79120.21351420.17081487100
5.7912-7.29250.2171450.17481520100
7.2925-49.20320.20291580.1755157499

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