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- PDB-1nj8: Crystal Structure of Prolyl-tRNA Synthetase from Methanocaldococc... -

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Basic information

Entry
Database: PDB / ID: 1nj8
TitleCrystal Structure of Prolyl-tRNA Synthetase from Methanocaldococcus janaschii
ComponentsProline-tRNA Synthetase
KeywordsLIGASE / Class-II tRNA synthetase
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Prolyl-tRNA synthetase, class II, C-terminal, archaeal-type / Prolyl-tRNA synthetase, C-terminal / C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) ...Prolyl-tRNA synthetase, class II, C-terminal, archaeal-type / Prolyl-tRNA synthetase, C-terminal / C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proline--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
Authors: Kamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A.
History
DepositionDec 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline-tRNA Synthetase
B: Proline-tRNA Synthetase
C: Proline-tRNA Synthetase
D: Proline-tRNA Synthetase


Theoretical massNumber of molelcules
Total (without water)215,1154
Polymers215,1154
Non-polymers00
Water1,69394
1
A: Proline-tRNA Synthetase
B: Proline-tRNA Synthetase


Theoretical massNumber of molelcules
Total (without water)107,5582
Polymers107,5582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-35 kcal/mol
Surface area39030 Å2
MethodPISA
2
C: Proline-tRNA Synthetase
D: Proline-tRNA Synthetase


Theoretical massNumber of molelcules
Total (without water)107,5582
Polymers107,5582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-35 kcal/mol
Surface area39020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.940, 104.845, 91.748
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological unit is a dimer. Each asymmetric unit contains two such dimers.

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Components

#1: Protein
Proline-tRNA Synthetase / E.C.6.1.1.15 / Prolyl-tRNA synthetase / Proline--tRNA ligase / ProRS


Mass: 53778.809 Da / Num. of mol.: 4
Fragment: N terminally His tagged and Thrombin digested enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Description: Strain supplemented with additional plasmid encoding rare tRNAs
Gene: MJ1238 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RecA- / References: UniProt: Q58635, proline-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 4.46 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium Acetate, Ammonium Sulfate, PEG 4000, beta-Mercaptoethanol, Tris, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 12-25 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMTris1droppH8.5
3200 mM1dropNaCl
45 mM2-mercaptoethanol1drop
50.2 Mammonium sulfate1reservoir
620-30 %PEG40001reservoir
75 mM2-mercaptoethanol1reservoir
80.1 M1reservoirpH4.5NaOAc

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.943
SYNCHROTRONALS 5.0.121.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 29, 2000
ADSC QUANTUM 42CCDMay 18, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)SINGLE WAVELENGTHMx-ray1
2Si(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9431
21.11
ReflectionResolution: 3.2→20 Å / Num. all: 34834 / Num. obs: 30271 / % possible obs: 86.9 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 80.3
Reflection
*PLUS
Highest resolution: 3.2 Å
Reflection shell
*PLUS
% possible obs: 80.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Thermus Thermophilus Proline tRNA Synthetase

Resolution: 3.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 225015.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2954 10 %RANDOM
Rwork0.231 ---
all0.2311 34036 --
obs0.2311 29611 87 %-
Solvent computationSolvent model: BULK SOLVENT MODELING / Bsol: 10 Å2 / ksol: 0.1854 e/Å3
Displacement parametersBiso mean: 65.4 Å2
Baniso -1Baniso -2Baniso -3
1--12.93 Å20 Å210.96 Å2
2---25.61 Å20 Å2
3---38.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15088 0 0 94 15182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it5.321.5
X-RAY DIFFRACTIONc_mcangle_it8.712
X-RAY DIFFRACTIONc_scbond_it7.512
X-RAY DIFFRACTIONc_scangle_it11.382.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 469 10.4 %
Rwork0.336 --
obs-4040 79.8 %
Refinement
*PLUS
Highest resolution: 3.2 Å / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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