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- PDB-6byq: Crystal structure of Tyrosine-tRNA ligase from Helicobacter pylori G27 -

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Basic information

Entry
Database: PDB / ID: 6byq
TitleCrystal structure of Tyrosine-tRNA ligase from Helicobacter pylori G27
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / SSGCID / Structural Genomics / Tyrosine--tRNA ligase / Helicobacter pylori / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 2 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / 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. / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / S4 RNA-binding domain ...Tyrosine-tRNA ligase, bacterial-type, type 2 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / 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. / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Tyrosine-tRNA ligase from Helicobacter pylori G27
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7932
Polymers46,7331
Non-polymers601
Water2,198122
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5854
Polymers93,4652
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2330 Å2
ΔGint-27 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.400, 43.360, 113.700
Angle α, β, γ (deg.)90.000, 121.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

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Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 46732.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: tyrS, HPG27_731 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B5Z7D7, tyrosine-tRNA ligase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.74 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions Morpheus screen D11: 10% w/V PEG 4000, 20% V/V glycerol, 0.02 M each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, M 2-propanol, 1,4-butanediol, 1,3-propanediol: ...Details: Molecular Dimensions Morpheus screen D11: 10% w/V PEG 4000, 20% V/V glycerol, 0.02 M each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, M 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM Bicine/Tris base pH 8.5: HepyC.00630.a.B1/HepyC.01032.a.B1.PS38283 at 18.5mg/ml: cryo: direct: tray 292683 d11: puck xoe2-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→40.011 Å / Num. obs: 25454 / % possible obs: 97.1 % / Redundancy: 4.17 % / Biso Wilson estimate: 40.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.056 / Χ2: 1.016 / Net I/σ(I): 18.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.263.7370.4982.616370.790.57884.8
2.26-2.323.9680.4653.0118030.830.53997.2
2.32-2.394.2910.3464.2918130.9250.39597.7
2.39-2.464.30.295.2216960.9450.33198
2.46-2.544.2730.2445.9816970.960.27997.4
2.54-2.634.2950.2027.0816080.9720.23198.2
2.63-2.734.30.1449.5915690.9870.16597.8
2.73-2.844.2820.10912.1315100.9920.12598.1
2.84-2.974.2450.09214.714600.9930.10598.1
2.97-3.114.2570.07317.6314110.9960.08398.3
3.11-3.284.2340.05722.4613120.9970.06598.5
3.28-3.484.2410.04328.112550.9980.04998.4
3.48-3.724.2030.03632.3811950.9980.04298.5
3.72-4.024.1580.03236.2311260.9990.03699
4.02-4.44.1130.02840.6510110.9990.03298.4
4.4-4.924.1220.02643.259480.9990.02998.8
4.92-5.684.0870.02541.758130.9990.02998.8
5.68-6.964.0470.02841.297160.9990.03298.5
6.96-9.843.980.02347.255550.9990.02798.2
9.84-40.0113.5830.0248.413190.9990.02394.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_2947refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
SIMBADphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1h3f as per MorDa, TARGET IDENTIFIED WITH SIMBAD

1h3f


Resolution: 2.2→40.011 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.77
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 1964 7.72 %0
Rwork0.1781 ---
obs0.1805 25445 97.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.38 Å2 / Biso mean: 60.732 Å2 / Biso min: 19.55 Å2
Refinement stepCycle: final / Resolution: 2.2→40.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 4 123 2493
Biso mean--50.4 55.31 -
Num. residues----313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.25510.25651390.22791434157384
2.2551-2.3160.27941470.23031644179198
2.316-2.38420.25541430.19861699184298
2.3842-2.46110.23631340.18981638177298
2.4611-2.54910.26611180.18691717183598
2.5491-2.65110.23781370.18881662179998
2.6511-2.77170.21581190.17421700181998
2.7717-2.91780.18561430.17841686182998
2.9178-3.10060.21961460.19031693183999
3.1006-3.33990.23871540.17781685183999
3.3399-3.67580.18631240.18361712183699
3.6758-4.20710.19911450.16941712185799
4.2071-5.29860.17841750.15021709188499
5.2986-40.0180.21121400.18221790193098
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)
13.4865-0.0388-0.72655.26650.24393.463-0.067-0.3261-0.01160.51910.10910.4554-0.1421-0.1727-0.02430.23710.02060.03810.2698-0.00790.2624-31.492-20.924811.0477
20.7172-0.5696-1.35634.03190.613.516-0.2746-0.2625-0.55530.41670.2055-0.9842-0.12551.01980.07050.39270.0021-0.10080.51860.05170.5045-10.5524-28.439413.9034
34.80180.1381-2.04212.1245-0.02231.94960.11-0.36970.37120.22470.0337-0.3753-0.05410.1963-0.13840.24790.0236-0.07310.3107-0.03310.4003-12.0458-21.22337.5054
42.5434-0.7291-0.3082.8068-0.80923.1106-0.4079-1.20390.05261.64430.52120.2848-0.128-0.2393-0.05881.06680.23570.09370.8424-0.04080.3185-30.1209-16.161128.4456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 69 )A-2 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 98 )A70 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 209 )A99 - 209
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 317 )A210 - 317

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