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- PDB-3wkr: Crystal structure of the SepCysS-SepCysE complex from Methanocald... -

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Basic information

Entry
Database: PDB / ID: 3wkr
TitleCrystal structure of the SepCysS-SepCysE complex from Methanocaldococcus jannaschii
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: 2.803 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 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 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

Downloads & links

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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
E: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
F: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
G: Uncharacterized protein MJ1481
H: Uncharacterized protein MJ1481


Theoretical massNumber of molelcules
Total (without water)291,0368
Polymers291,0368
Non-polymers00
Water2,036113
1
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)145,5184
Polymers145,5184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-96 kcal/mol
Surface area34220 Å2
MethodPISA
2
E: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
F: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
G: Uncharacterized protein MJ1481
H: Uncharacterized protein MJ1481


Theoretical massNumber of molelcules
Total (without water)145,5184
Polymers145,5184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-94 kcal/mol
Surface area34460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.880, 106.880, 495.253
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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.: 4
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: 25334.650 Da / Num. of mol.: 4
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.: 113 / 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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Ammonium citrate, PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2012
RadiationMonochromator: Si (11 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.498
ReflectionResolution: 2.8→47.3 Å / Num. obs: 74017 / % possible obs: 95 % / Redundancy: 4.11 % / Rsym value: 0.109 / Net I/σ(I): 9.28
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.16 % / Rmerge F obs: 0.608 / Mean I/σ(I) obs: 1.48 / Num. measured obs: 38762 / Num. possible: 6732 / Num. unique obs: 6424 / Rrim(I) all: 0.706 / Rsym value: 0.623 / % possible all: 94.6

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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: 2.803→47.3 Å / FOM work R set: 0.8219 / σ(F): 1.39 / Phase error: 25.82 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2425 4303 5.81 %
Rwork0.2244 --
obs0.2297 74017 94.92 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.184 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 245.58 Å2 / Biso mean: 101.35 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.4783 Å20 Å2-0 Å2
2---0.4783 Å20 Å2
3---0.9566 Å2
Refinement stepCycle: LAST / Resolution: 2.803→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13917 0 0 113 14030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214191
X-RAY DIFFRACTIONf_angle_d0.53419058
X-RAY DIFFRACTIONf_chiral_restr0.0352058
X-RAY DIFFRACTIONf_plane_restr0.0032411
X-RAY DIFFRACTIONf_dihedral_angle_d10.2625441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8036-2.85190.33511990.32333285348485
2.8519-2.90380.32772400.31043518375890
2.9038-2.95960.30042130.30673562377591
2.9596-3.020.31521990.30313525372492
3.02-3.08560.29522210.2983564378591
3.0856-3.15730.30062210.29283541376291
3.1573-3.23620.33352130.27943574378791
3.2362-3.32370.27512060.26653522372891
3.3237-3.42140.27491990.26513530372991
3.4214-3.53170.27542240.2513523374790
3.5317-3.65780.27892170.24873494371190
3.6578-3.80410.26362140.23653516373090
3.8041-3.9770.25512180.22663399361787
3.977-4.18640.22772090.21693447365689
4.1864-4.44820.24592180.21373515373390
4.4482-4.79080.19912090.2013458366789
4.7908-5.27150.2312070.20393486369389
5.2715-6.03090.2312050.20633454365989
6.0309-7.58540.23132250.20333401362687
7.5854-34.90040.20462220.18423398362087

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