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- PDB-3sz3: Crystal structure of Tryptophanyl-tRNA synthetase from Vibrio cho... -

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Basic information

Entry
Database: PDB / ID: 3sz3
TitleCrystal structure of Tryptophanyl-tRNA synthetase from Vibrio cholerae with an endogenous tryptophan
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Rossmann Fold
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) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle ...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) / 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 speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCooper, D.R. / Kudritska, M. / Chruszcz, M. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of Tryptophanyl-tRNA synthetase from Vibrio cholerae with an endogenous tryptophan
Authors: Cooper, D.R. / Kudritska, M. / Chruszcz, M. / Grabowski, M. / Anderson, W.F. / Minor, W.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0433
Polymers37,7471
Non-polymers2962
Water7,764431
1
A: Tryptophanyl-tRNA synthetase
hetero molecules

A: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0876
Polymers75,4942
Non-polymers5934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4960 Å2
ΔGint-37 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.020, 94.047, 47.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 37747.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: trpS, VC_2623 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9KNV7, tryptophan-tRNA ligase
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: 60% Tascimate, pH 7, vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 11, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 54037 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.041 / Χ2: 0.93 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.535.90.40326460.562198.5
1.53-1.556.10.34626180.558198.6
1.55-1.586.20.30226660.574199.2
1.58-1.626.30.2626740.603199.4
1.62-1.656.40.23226560.62199.5
1.65-1.696.50.226550.637199.6
1.69-1.736.50.17326740.682199.7
1.73-1.786.60.15226540.695199.7
1.78-1.836.70.11926910.738199.8
1.83-1.896.70.09926910.778199.8
1.89-1.966.80.08227030.824199.7
1.96-2.046.90.06426800.898199.9
2.04-2.1370.05326950.951199.9
2.13-2.247.10.04627060.9941100
2.24-2.387.20.0427251.0381100
2.38-2.567.30.03627131.071100
2.56-2.827.30.03127311.1261100
2.82-3.237.30.02727701.2211100
3.23-4.077.20.02527831.5021100
4.07-406.70.03129062.069198.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N9I

3n9i


Resolution: 1.5→26.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1805 / WRfactor Rwork: 0.1597 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8963 / SU B: 2.43 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0711 / SU Rfree: 0.0689 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2745 5.1 %RANDOM
Rwork0.1596 ---
obs0.1606 53996 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.33 Å2 / Biso mean: 22.8065 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.26 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 17 431 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222870
X-RAY DIFFRACTIONr_bond_other_d0.0010.021919
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9663922
X-RAY DIFFRACTIONr_angle_other_deg0.90934706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9724.729129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26815482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3681517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
X-RAY DIFFRACTIONr_mcbond_it0.8061.51815
X-RAY DIFFRACTIONr_mcbond_other0.2161.5720
X-RAY DIFFRACTIONr_mcangle_it1.40722943
X-RAY DIFFRACTIONr_scbond_it2.10531055
X-RAY DIFFRACTIONr_scangle_it3.3724.5977
LS refinement shellResolution: 1.503→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 192 -
Rwork0.185 3499 -
all-3691 -
obs--92.81 %
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)
10.26320.3139-0.12510.7801-0.1460.29020.0088-0.00140.05230.01450.0082-0.0133-0.0406-0.028-0.0170.0257-0.0048-0.00820.03310.00990.03154.35320.61119.119
24.61792.034-2.77163.97332.54526.27610.0761-0.2709-0.14080.0022-0.1852-0.0466-0.08070.07550.10910.048-0.0063-0.01030.04560.01820.0414.2937.94323.752
30.5720.0913-0.1150.9860.26050.5273-0.01180.16380.0936-0.20790.02340.0558-0.0068-0.0043-0.01150.0783-0.0051-0.0220.06550.02680.0214-6.2879.3657.434
42.0073-1.91770.21095.2547-1.42011.30940.38320.40540.2754-0.5988-0.5038-0.29710.05780.04060.12060.11510.08430.05780.10510.0550.050413.45142.9925.582
50.8408-0.4720.28394.9999-3.36882.83660.0686-0.14150.04160.248-0.1776-0.181-0.23820.08290.10910.0498-0.0372-0.02960.06660.02890.065716.25326.74725.539
63.0682.12431.49232.1791.04330.90130.0481-0.17290.04730.0878-0.1170.07160.0056-0.03360.06890.0313-0.0184-0.0020.04610.00750.0153-2.3688.84326.903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 83
2X-RAY DIFFRACTION2A84 - 85
3X-RAY DIFFRACTION3A86 - 181
4X-RAY DIFFRACTION4A189 - 288
5X-RAY DIFFRACTION5A289 - 303
6X-RAY DIFFRACTION6A304 - 333

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