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- PDB-3m5w: Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobac... -

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Basic information

Entry
Database: PDB / ID: 3m5w
TitleCrystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / alpha-beta structure / CSGID / Aminoacyl-tRNA synthetase / ATP-binding / Nucleotide-binding / Protein biosynthesis / Structural Genomics / Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsKim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2010
Title: Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni
Authors: Kim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 1, 2014Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,50410
Polymers73,7472
Non-polymers7578
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-97 kcal/mol
Surface area29670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.153, 50.604, 108.640
Angle α, β, γ (deg.)90.00, 107.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase / TrpRS


Mass: 36873.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj0388, trpS / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PIB4, tryptophan-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25 % w/v Polyehtlyene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010 / Details: mirrors
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 29722 / Num. obs: 29722 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 48.3 Å2 / Rsym value: 0.131 / Net I/σ(I): 9.6
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1438 / Rsym value: 0.707 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→47.811 Å / SU ML: 0.33 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1997 6.88 %random
Rwork0.183 ---
all0.187 29037 --
obs0.187 29037 96.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.821 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.6726 Å20 Å2-7.6739 Å2
2--0.476 Å20 Å2
3---2.1935 Å2
Refinement stepCycle: LAST / Resolution: 2.32→47.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5001 0 43 215 5259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145210
X-RAY DIFFRACTIONf_angle_d1.4627012
X-RAY DIFFRACTIONf_dihedral_angle_d19.571935
X-RAY DIFFRACTIONf_chiral_restr0.094759
X-RAY DIFFRACTIONf_plane_restr0.006895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3204-2.40330.33851690.252381255086
2.4033-2.49960.31771920.23512590278294
2.4996-2.61330.31051990.23442679287896
2.6133-2.75110.3132000.22672672287296
2.7511-2.92340.3092000.21692732293298
2.9234-3.14910.24742020.20262767296999
3.1491-3.46590.24712050.189727592964100
3.4659-3.96720.24022090.15772777298699
3.9672-4.99740.17712080.13642818302699
4.9974-47.82110.21932130.1742865307899
Refinement TLS params.

S21: -0.0216 Å ° / Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.94320.47590.98640.37870.65121.1847-0.01020.16150.03270.0805-0.054-0.01780.1878-0.05840.1236-0.01310.0060.16420.03490.167535.12053.477720.3906
21.33780.44080.99250.06610.05960.73110.0894-0.0937-0.1365-0.0307-0.07130.117-0.0891-0.06390.2334-0.0031-0.01670.2175-0.01330.2281
Refinement TLS groupSelection details: chain B

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