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

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Basic information

Entry
Database: PDB / ID: 3tzl
TitleCrystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni complexed with ADP and Tryptophane
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / cytosol
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / 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 ...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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / TRYPTOPHAN / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.154 Å
AuthorsKim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni complexed with ADP and Tryptophane
Authors: Kim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,43612
Polymers73,7472
Non-polymers1,68910
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-78 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.777, 50.629, 105.915
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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 subsp. 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

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Non-polymers , 5 types, 228 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 4, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 36400 / Num. obs: 36400 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 37.8 Å2 / Rsym value: 0.107 / Net I/σ(I): 15.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.47 / Num. unique all: 1788 / Rsym value: 0.513 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.154→28.794 Å / SU ML: 0.52 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1810 4.99 %random
Rwork0.181 ---
all0.183 36301 --
obs0.183 36301 98.09 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.798 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.4883 Å2-0 Å2-1.3216 Å2
2---5.2424 Å2-0 Å2
3---8.7307 Å2
Refinement stepCycle: LAST / Resolution: 2.154→28.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 106 218 5411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095309
X-RAY DIFFRACTIONf_angle_d1.1897159
X-RAY DIFFRACTIONf_dihedral_angle_d15.4171991
X-RAY DIFFRACTIONf_chiral_restr0.069777
X-RAY DIFFRACTIONf_plane_restr0.004903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1538-2.2120.28291130.23992186229982
2.212-2.27710.27721190.223326932812100
2.2771-2.35060.26431540.220226622816100
2.3506-2.43450.29171260.21772695282199
2.4345-2.53190.26411440.21372685282999
2.5319-2.64710.3051440.217826482892100
2.6471-2.78660.28671600.21882673283399
2.7866-2.9610.26741230.2182688281199
2.961-3.18930.25691420.210427012843100
3.1893-3.50980.24121320.190927042835100
3.5098-4.01650.19371410.15742688282999
4.0165-5.05590.17061440.13452722286699
5.0559-28.79650.17051680.16012746291499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (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)
14.21190.00862.39860.72450.66422.4452-0.1020.42340.62420.00530.0749-0.1726-0.27810.23020.09670.3268-0.00730.0760.35050.05310.43343.087125.052632.22
23.03750.21790.70021.76420.5551.6855-0.0187-0.02850.4789-0.01040.0393-0.02-0.14530.07730.10720.2215-0.0150.01860.21750.01450.281833.305822.383936.0418
32.79830.7960.17022.04980.28731.364-0.03920.1619-0.2536-0.0920.0422-0.2435-0.01560.3482-0.02190.27070.00190.04080.30180.04810.277232.185510.173922.831
44.84150.38951.45341.62950.47072.5909-0.12940.70240.3602-0.27670.0732-0.2622-0.28920.52770.07940.3653-0.0220.10330.44730.10160.377735.983517.893315.4408
54.23930.05180.59131.57050.2081.3993-0.0309-0.19770.4412-0.06510.152-0.2763-0.13350.2878-0.04180.3256-0.0366-0.02860.3616-0.09230.427460.065324.128543.9972
62.70390.97311.55171.16470.78271.7655-0.1183-0.21780.4171-0.0862-0.19870.1215-0.1197-0.0390.3170.2980.02650.00380.27320.05390.388224.488723.995529.2372
72.77080.06681.32190.5151-0.05941.11480.04320.0334-0.1452-0.0932-0.09520.07270.1408-0.1594-0.00760.3013-0.01090.01690.2361-0.01790.250110.21060.375423.8343
82.37680.91671.42710.57341.12082.25670.3307-0.1609-0.85960.131-0.2254-0.04560.7346-0.0748-0.32090.4504-0.01740.00350.2412-0.01650.501812.8504-9.62528.5384
92.49211.22651.91680.95370.97392.4465-0.02190.0435-0.2394-0.11180.0691-0.03420.1824-0.28990.0070.3235-0.04840.04850.3367-0.04910.2718-7.745-4.549913.5783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:28)
2X-RAY DIFFRACTION2chain 'A' and (resseq 29:82)
3X-RAY DIFFRACTION3chain 'A' and (resseq 83:143)
4X-RAY DIFFRACTION4chain 'A' and (resseq 144:179)
5X-RAY DIFFRACTION5chain 'A' and (resseq 180:287)
6X-RAY DIFFRACTION6chain 'A' and (resseq 288:331)
7X-RAY DIFFRACTION7chain 'B' and (resseq 0:143)
8X-RAY DIFFRACTION8chain 'B' and (resseq 144:189)
9X-RAY DIFFRACTION9chain 'B' and (resseq 190:331)

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