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- PDB-2du7: Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA... -

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Basic information

Entry
Database: PDB / ID: 2du7
TitleCrystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase
ComponentsO-phosphoseryl-tRNA synthetase
KeywordsLIGASE / alpha4 tetramer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
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) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) ...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) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
O-phosphoserine--tRNA(Cys) ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFukunaga, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
Authors: Fukunaga, R. / Yokoyama, S.
History
DepositionJul 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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
A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
C: O-phosphoseryl-tRNA synthetase
D: O-phosphoseryl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)254,1104
Polymers254,1104
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26990 Å2
ΔGint-161 kcal/mol
Surface area116630 Å2
MethodPISA, PQS
2
A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
C: O-phosphoseryl-tRNA synthetase
D: O-phosphoseryl-tRNA synthetase

A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
C: O-phosphoseryl-tRNA synthetase
D: O-phosphoseryl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)508,2218
Polymers508,2218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area63650 Å2
ΔGint-375 kcal/mol
Surface area223580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.354, 299.455, 125.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
O-phosphoseryl-tRNA synthetase / Putative phenylalanyl-tRNA synthetase alpha chain-like protein MJ1660


Mass: 63527.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET26b / Production host: Escherichia coli (E. coli)
References: UniProt: Q59054, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds

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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: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 11.25% PEG 4000, 75mM Na-citrate, 75mM ADA-NaOH buffer (pH 6.7), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. all: 43084 / Num. obs: 42030 / % possible obs: 97.6 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.6→3.73 Å / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DU3

2du3


Resolution: 3.6→19.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 7089748.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.387 4236 10.1 %RANDOM
Rwork0.33 ---
obs0.33 42030 97.5 %-
all-43084 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9985 Å2 / ksol: 0.194656 e/Å3
Displacement parametersBiso mean: 129.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.16 Å20 Å20 Å2
2---3.37 Å20 Å2
3----8.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a1 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 3.6→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17516 0 0 0 17516
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it23.171.5
X-RAY DIFFRACTIONc_mcangle_it35.92
X-RAY DIFFRACTIONc_scbond_it28.242
X-RAY DIFFRACTIONc_scangle_it41.272.5
LS refinement shellResolution: 3.6→3.82 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 669 10 %
Rwork0.373 6045 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna_rep.top

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