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- PDB-5tev: Crystal structure of a tryptophanyl-tRNA synthetase from Neisseri... -

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Basic information

Entry
Database: PDB / ID: 5tev
TitleCrystal structure of a tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae, apo
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / NIAID / structural genomics / aaRS / aminoacyl tRNA synthetase / tRNA ligase / tryptophan / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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) / 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--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae, apo
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionSep 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,3122
Polymers77,3122
Non-polymers00
Water4,666259
1
A: Tryptophan--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)38,6561
Polymers38,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tryptophan--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)38,6561
Polymers38,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 59.940, 355.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-460-

HOH

31A-532-

HOH

41B-437-

HOH

51B-478-

HOH

61B-511-

HOH

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Components

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


Mass: 38655.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: trpS, NGO_1045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F7X0, tryptophan-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NegoA.00743.a.B1.PS37949 at 19.2 mg/mL against Morpheus screen condition G9 10% PEG 20,000, 20% PEG 550 MME, 0.02 M carboxylates, 0.1 M bicine/trizma pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 36620 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 35.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.42
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.25-2.310.5573.490.889199.9
2.31-2.370.4714.170.928199.8
2.37-2.440.3994.850.941199.7
2.44-2.520.3265.780.959199.8
2.52-2.60.2647.210.974199.8
2.6-2.690.2138.770.982199.9
2.69-2.790.17510.390.986199.8
2.79-2.90.15311.940.989199.9
2.9-3.030.12314.470.993199.8
3.03-3.180.10217.250.994199.8
3.18-3.350.08820.060.995199.7
3.35-3.560.07223.880.997199.9
3.56-3.80.06526.490.997199.8
3.8-4.110.05728.460.998199.9
4.11-4.50.05130.870.998199.1
4.5-5.030.04831.610.998199.7
5.03-5.810.04630.030.998199.9
5.81-7.120.04330.480.999199.3
7.12-10.060.03733.030.999198.9
10.060.03730.60.999194.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(DEV_2499: ???)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TZL

3tzl


Resolution: 2.25→44.828 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.86
RfactorNum. reflection% reflection
Rfree0.2368 2021 5.52 %
Rwork0.175 --
obs0.1784 36609 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.72 Å2 / Biso mean: 45.2911 Å2 / Biso min: 15.89 Å2
Refinement stepCycle: final / Resolution: 2.25→44.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 0 259 5330
Biso mean---41.25 -
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075195
X-RAY DIFFRACTIONf_angle_d0.7927068
X-RAY DIFFRACTIONf_chiral_restr0.048800
X-RAY DIFFRACTIONf_plane_restr0.005937
X-RAY DIFFRACTIONf_dihedral_angle_d14.5693156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2498-2.30610.27931140.205624872601100
2.3061-2.36850.2791400.202323982538100
2.3685-2.43810.28581310.204623952526100
2.4381-2.51680.25891800.19724022582100
2.5168-2.60680.23891430.185824602603100
2.6068-2.71110.26311510.186823922543100
2.7111-2.83450.26711320.197824562588100
2.8345-2.98390.26831400.213624562596100
2.9839-3.17080.29911550.207924502605100
3.1708-3.41560.27961490.199724342583100
3.4156-3.75910.20571740.169324842658100
3.7591-4.30270.18841530.142525082661100
4.3027-5.41950.20221220.142225642686100
5.4195-44.83670.21441370.15842702283998
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)
13.56860.66311.31842.1029-0.79135.27370.0054-0.00640.097-0.06830.0295-0.1216-0.2050.2441-0.01650.2942-0.01590.00780.1901-0.00880.3134.9842-12.1483-53.2079
23.70771.06692.32616.15893.57473.59120.1203-0.3825-0.36440.677-0.34640.19120.1359-0.3440.15220.329-0.01010.01430.34890.02120.284124.7079-19.7899-43.9475
31.54970.7237-0.16771.9384-0.15680.7066-0.0969-0.1371-0.16650.0480.0428-0.23910.04220.1310.04150.22070.00160.04830.27940.02230.280726.8144-27.6747-57.274
43.96810.91660.60112.3701-0.17520.8008-0.00040.1712-0.3429-0.15530.1338-0.3744-0.12040.2986-0.08910.2883-0.02940.11980.30160.00230.317432.7968-24.4116-67.1943
52.3682-0.93241.3823.08960.99372.5273-0.4808-0.7439-0.55390.16030.4639-0.4572-0.26950.85350.03330.36280.05620.01840.86840.21190.49946.8016-19.5271-32.6751
63.68730.16691.78693.29471.17261.53410.1162-0.11410.4416-0.48170.1815-1.3067-0.27120.7344-0.12870.391-0.19150.03471.2292-0.0130.679956.9975-13.2261-37.3101
72.43260.5210.6221.43740.05051.4298-0.1938-0.30240.29450.0520.0378-0.0959-0.50240.17040.21370.2829-0.00690.01610.28560.01840.242426.6577-10.5767-50.1402
83.1906-1.3212-1.22651.58791.01141.8504-0.21120.2251-0.17110.05420.0547-0.06930.1042-0.12820.1590.3021-0.0402-0.0180.28460.02360.237259.2908-34.4011-6.9217
92.8901-1.36530.06592.4242-0.12450.3596-0.23490.08230.61230.18320.143-0.49-0.09710.11210.08140.33520.0123-0.1690.38520.00170.442262.0971-19.69891.7272
104.53340.9273-2.03322.4887-0.30434.13470.1639-0.12620.21290.2162-0.1725-0.4375-0.1610.1603-0.01420.3266-0.0269-0.00940.30820.10310.368981.0561-33.1239-26.098
113.5675-0.8103-2.3371.25720.59522.4058-0.37120.1201-0.45020.1849-0.0565-0.05410.3558-0.1110.43410.309-0.0153-0.08020.20960.09090.228664.3231-40.1344-12.1774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 43 )A3 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 71 )A44 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 157 )A72 - 157
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 193 )A158 - 193
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 240 )A194 - 240
6X-RAY DIFFRACTION6chain 'A' and (resid 241 through 271 )A241 - 271
7X-RAY DIFFRACTION7chain 'A' and (resid 272 through 336 )A272 - 336
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 100 )B2 - 100
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 193 )B101 - 193
10X-RAY DIFFRACTION10chain 'B' and (resid 194 through 255 )B194 - 255
11X-RAY DIFFRACTION11chain 'B' and (resid 256 through 336 )B256 - 336

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