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- PDB-2du5: Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA s... -

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Basic information

Entry
Database: PDB / ID: 2du5
TitleCrystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N mutant complexed with tRNAOpal and O-phosphoserine ("opal complex")
Components
  • O-phosphoseryl-tRNA synthetase
  • tRNA
KeywordsLIGASE/RNA / alpha4 tetramer / LIGASE-RNA COMPLEX
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 / identical protein binding / cytoplasm
Similarity search - Function
Double Stranded RNA Binding Domain - #20 / O-phosphoseryl-tRNA(Cys) ligase / O-phosphoserine--tRNA(Cys) ligase, C-terminal domain / O-phosphoseryl-tRNA synthetase C-terminal domain / Double Stranded RNA Binding Domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Other non-globular / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Double Stranded RNA Binding Domain - #20 / O-phosphoseryl-tRNA(Cys) ligase / O-phosphoserine--tRNA(Cys) ligase, C-terminal domain / O-phosphoseryl-tRNA synthetase C-terminal domain / Double Stranded RNA Binding Domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Other non-globular / 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) / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOSERINE / RNA / RNA (> 10) / O-phosphoserine--tRNA(Cys) ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFukunaga, R.
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 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: tRNA
A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7345
Polymers145,3643
Non-polymers3702
Water00
1
D: tRNA
A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
hetero molecules

D: tRNA
A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,46810
Polymers290,7286
Non-polymers7404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)148.040, 148.040, 152.483
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a tetramer of O-phosphoseryl-tRNA synthetase with two bound tRNAOpal molecules generated from the dimer O-phosphoseryl-tRNA synthetase with one bound tRNAOpal molecule in the asymmetric unit by the operations: y, x, -z

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Components

#1: RNA chain tRNA


Mass: 22893.566 Da / Num. of mol.: 1 / Mutation: G33U / Source method: obtained synthetically
#2: Protein O-phosphoseryl-tRNA synthetase


Mass: 61235.133 Da / Num. of mol.: 2 / Mutation: E418N, E420N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET26b / Production host: Escherichia coli (E. coli)
References: UniProt: O30126, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds
#3: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8NO6P

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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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% PEG 6000, 1.2M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2NaCl11
3PEG 600012
4NaCl12

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 32318 / Num. obs: 32270 / % possible obs: 99.9 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.31 Å / % possible all: 99.8

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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: 3.2→49.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4343279.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1603 5 %RANDOM
Rwork0.223 ---
obs0.223 32270 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 101.557 Å2 / ksol: 0.285269 e/Å3
Displacement parametersBiso mean: 113.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å212.13 Å20 Å2
2---4.74 Å20 Å2
3---9.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8080 1517 22 0 9619
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it20.51.5
X-RAY DIFFRACTIONc_mcangle_it23.982
X-RAY DIFFRACTIONc_scbond_it27.42
X-RAY DIFFRACTIONc_scangle_it29.732.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 252 4.8 %
Rwork0.286 5039 -
obs--99.7 %
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
X-RAY DIFFRACTION5SEP.param

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