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- PDB-3dsq: Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl tRN... -

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Basic information

Entry
Database: PDB / ID: 3dsq
TitleStructure of Desulfitobacterium hafniense PylSc, a pyrrolysyl tRNA synthetase
ComponentsPyrrolysyl-tRNA synthetasePyrrolysine—tRNAPyl ligase
KeywordsLIGASE / homodimer / Aminoacyl-tRNA synthetase
Function / homology
Function and homology information


tRNA aminoacylation / aminoacyl-tRNA ligase activity / transferase activity / tRNA binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / 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) / Helix Hairpins ...Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pyrrolysyl-tRNA synthetase
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, M.M. / Chan, M.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl-tRNA synthetase.
Authors: Lee, M.M. / Jiang, R. / Jain, R. / Larue, R.C. / Krzycki, J. / Chan, M.K.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolysyl-tRNA synthetase
B: Pyrrolysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6794
Polymers66,6212
Non-polymers582
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-43 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.183, 68.467, 96.288
Angle α, β, γ (deg.)90.00, 136.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pyrrolysyl-tRNA synthetase / Pyrrolysine—tRNAPyl ligase


Mass: 33310.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Gene: pylS / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0S4P3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 M potassium sodium tartrate, 0.1 M Tris pH 8.5, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→58.1 Å / Num. all: 34245 / Num. obs: 34081 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.096 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2490 / Rsym value: 0.343 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q7H

2q7h


Resolution: 2.1→36.32 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1813236.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1720 5 %RANDOM
Rwork0.235 ---
all0.237 34245 --
obs0.235 34078 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5158 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--9.39 Å20 Å2-2.45 Å2
2---12.02 Å20 Å2
3---21.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.1→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4543 0 2 163 4708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 279 4.9 %
Rwork0.332 5366 -
obs-5366 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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