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- PDB-6dfu: Tryptophan--tRNA ligase from Haemophilus influenzae. -

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Basic information

Entry
Database: PDB / ID: 6dfu
TitleTryptophan--tRNA ligase from Haemophilus influenzae.
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / structural genomics / IDP07216 / tRNA ligase / tryptophan / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol
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 / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOsipiuk, J. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: to be published
Title: Tryptophan--tRNA ligase from Haemophilus influenzae.
Authors: Osipiuk, J. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase
B: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8374
Polymers75,4282
Non-polymers4082
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-30 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.294, 48.677, 99.322
Angle α, β, γ (deg.)90.000, 101.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37714.070 Da / Num. of mol.: 2 / Mutation: 3 N-terminal residues, SNA, are cloning artifacts
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trpS, HI_0637 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43835, tryptophan-tRNA ligase
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1 M potassium thiocyanate, 30% PEG MME 2000, 10 mM tryptophane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 13, 2017
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 42196 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.071 / Rrim(I) all: 0.141 / Χ2: 1.693 / Net I/σ(I): 8.9 / Num. measured all: 160897
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.093.40.64220710.8750.4010.761.22999.3
2.09-2.123.70.57621140.790.3430.6721.23699.8
2.12-2.163.80.5420570.8050.320.631.327100
2.16-2.213.80.51121180.7910.3030.5951.362100
2.21-2.263.80.46420850.8590.2730.541.431100
2.26-2.313.80.38421110.9290.2250.4451.435100
2.31-2.373.80.36720750.9260.2150.4271.498100
2.37-2.433.90.33121240.9330.1940.3841.568100
2.43-2.53.90.29620810.9380.1740.3441.604100
2.5-2.583.90.25421030.9550.1490.2951.691100
2.58-2.683.90.22220980.960.130.2571.729100
2.68-2.783.90.20221030.9640.1190.2351.847100
2.78-2.913.90.17921000.9730.1040.2071.906100
2.91-3.063.90.15621310.9780.0920.1822.028100
3.06-3.253.90.12421050.9850.0720.1442.042100
3.25-3.513.90.10521220.9840.060.1211.97100
3.51-3.863.90.09321150.9890.0540.1071.967100
3.86-4.423.90.07921320.9930.0460.0912.012100
4.42-5.563.80.07221480.9920.0420.0831.915100
5.56-503.70.06522030.9930.0390.0761.87298.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N9I

3n9i


Resolution: 2.05→35.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.513 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.184
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2084 4.9 %RANDOM
Rwork0.1872 ---
obs0.1897 40090 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.82 Å2 / Biso mean: 37.432 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0 Å20.28 Å2
2--0.23 Å20 Å2
3---0.81 Å2
Refinement stepCycle: final / Resolution: 2.05→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5225 0 30 196 5451
Biso mean--37.48 38.66 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195487
X-RAY DIFFRACTIONr_bond_other_d0.0020.025177
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9647459
X-RAY DIFFRACTIONr_angle_other_deg0.984312042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85424.866261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16415988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2571532
X-RAY DIFFRACTIONr_chiral_restr0.090.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216119
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021077
LS refinement shellResolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 101 -
Rwork0.265 2218 -
all-2319 -
obs--74.11 %
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)
10.07170.04320.21150.03440.11860.75750.01920.0285-0.0105-0.00980.0337-0.00730.0473-0.0744-0.05290.06370.00670.00520.25750.02140.0061-13.953-7.73586.1414
20.16520.12120.23170.09690.15910.44290.0254-0.0239-0.01430.01990.0111-0.0177-0.0219-0.0297-0.03650.0460.01120.01230.214-0.01280.0255.70918.257245.1898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 501
2X-RAY DIFFRACTION2B2 - 501

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