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- PDB-5x6c: Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 5x6c
TitleCrystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii
Components
  • O-phosphoserine--tRNA(Cys) ligase
  • Uncharacterized protein MJ1481
KeywordsRNA BINDING PROTEIN / O-phosphoseryl-tRNA synthetase / multiple domain protein / coiled-coil insertion
Function / homology
Function and homology information


O-phospho-L-serine-tRNA ligase / phosphoserine-tRNA(Cys) ligase activity / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Uncharacterised protein MJ1481, archaea / Uncharacterized protein conserved in archaea (DUF2100) / O-phosphoseryl-tRNA(Cys) ligase / O-phosphoserine--tRNA(Cys) ligase, C-terminal domain / O-phosphoseryl-tRNA synthetase C-terminal domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein MJ1481 / O-phosphoserine--tRNA(Cys) ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
Methanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 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

Downloads & links

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Assembly

Deposited unit
A: O-phosphoserine--tRNA(Cys) ligase
B: O-phosphoserine--tRNA(Cys) ligase
E: Uncharacterized protein MJ1481
F: Uncharacterized protein MJ1481
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6568
Polymers178,4494
Non-polymers1,2064
Water1,964109
1
A: O-phosphoserine--tRNA(Cys) ligase
B: O-phosphoserine--tRNA(Cys) ligase
E: Uncharacterized protein MJ1481
F: Uncharacterized protein MJ1481
hetero molecules

A: O-phosphoserine--tRNA(Cys) ligase
B: O-phosphoserine--tRNA(Cys) ligase
E: Uncharacterized protein MJ1481
F: Uncharacterized protein MJ1481
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,31116
Polymers356,8998
Non-polymers2,4138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_545-x,-y-1/2,z1
Buried area45500 Å2
ΔGint-283 kcal/mol
Surface area87930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.821, 279.821, 279.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein O-phosphoserine--tRNA(Cys) ligase / O-phosphoserine--tRNA ligase / Non-canonical O-phosphoseryl-tRNA(Cys) synthetase / O-phosphoseryl- ...O-phosphoserine--tRNA ligase / Non-canonical O-phosphoseryl-tRNA(Cys) synthetase / O-phosphoseryl-tRNA(Cys) synthetase / SepRS


Mass: 63889.977 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: MJ1660 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59054*PLUS, O-phospho-L-serine-tRNA ligase
#2: Protein Uncharacterized protein MJ1481


Mass: 25334.650 Da / Num. of mol.: 2 / Fragment: UNP residues 1-24
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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 5.12 Å3/Da / Density % sol: 82.41 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 0.1M Tris-HCl pH7.0, 0.3M Ammonium sulfate, 36% MPD
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48 Å / Num. obs: 65670 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DU7

2du7


Resolution: 3.101→47.989 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.2092 3328 5.07 %
Rwork0.1847 --
obs0.186 65625 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.101→47.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 0 72 109 9363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149436
X-RAY DIFFRACTIONf_angle_d1.34612726
X-RAY DIFFRACTIONf_dihedral_angle_d16.263662
X-RAY DIFFRACTIONf_chiral_restr0.0631400
X-RAY DIFFRACTIONf_plane_restr0.0061614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1011-3.14540.31951480.28522548X-RAY DIFFRACTION99
3.1454-3.19230.29041420.26732599X-RAY DIFFRACTION100
3.1923-3.24220.27631220.27562559X-RAY DIFFRACTION100
3.2422-3.29530.28771310.26452593X-RAY DIFFRACTION100
3.2953-3.35220.30591340.25922554X-RAY DIFFRACTION100
3.3522-3.41310.28841500.24672639X-RAY DIFFRACTION100
3.4131-3.47870.2691340.22542526X-RAY DIFFRACTION100
3.4787-3.54970.28461410.22322571X-RAY DIFFRACTION100
3.5497-3.62690.2741420.21222622X-RAY DIFFRACTION100
3.6269-3.71120.20921420.19622557X-RAY DIFFRACTION100
3.7112-3.8040.23591430.1842600X-RAY DIFFRACTION100
3.804-3.90680.18371440.18262563X-RAY DIFFRACTION100
3.9068-4.02170.20141300.16332603X-RAY DIFFRACTION100
4.0217-4.15140.18311390.15822589X-RAY DIFFRACTION100
4.1514-4.29970.17411410.1442587X-RAY DIFFRACTION100
4.2997-4.47170.16471410.14792593X-RAY DIFFRACTION100
4.4717-4.67510.16291320.13612598X-RAY DIFFRACTION100
4.6751-4.92130.16741490.14172610X-RAY DIFFRACTION100
4.9213-5.22930.18921340.16172597X-RAY DIFFRACTION100
5.2293-5.63250.19061310.17272625X-RAY DIFFRACTION100
5.6325-6.19830.21631410.19382612X-RAY DIFFRACTION100
6.1983-7.09270.24491350.20742625X-RAY DIFFRACTION100
7.0927-8.92670.15611240.15642673X-RAY DIFFRACTION100
8.9267-47.99460.18371580.18012654X-RAY DIFFRACTION98

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