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- PDB-6wom: Crystal structure of Aspartyl-tRNA ligase from Elizabethkingia sp. -

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Basic information

Entry
Database: PDB / ID: 6wom
TitleCrystal structure of Aspartyl-tRNA ligase from Elizabethkingia sp.
ComponentsAspartate--tRNA ligase
KeywordsLIGASE / SSGCID / Structural Genomics / Elizabethkingia sp. / AspRS / Aspartyl-tRNA ligase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II ...Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Aspartate--tRNA ligase
Similarity search - Component
Biological speciesElizabethkingia anophelis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Aspartyl-tRNA ligase from Elizabethkingia sp.
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate--tRNA ligase
B: Aspartate--tRNA ligase
C: Aspartate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,0975
Polymers202,9043
Non-polymers1922
Water18,7001038
1
A: Aspartate--tRNA ligase
B: Aspartate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,4624
Polymers135,2702
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-65 kcal/mol
Surface area48610 Å2
MethodPISA
2
C: Aspartate--tRNA ligase

C: Aspartate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)135,2702
Polymers135,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8620 Å2
ΔGint-53 kcal/mol
Surface area46330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.370, 106.570, 93.410
Angle α, β, γ (deg.)90.000, 100.910, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 8 or (resid 9...
21(chain B and (resid 1 through 8 or (resid 9...
31(chain C and (resid 1 through 97 or resid 99...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and (resid 1 through 8 or (resid 9...AA08
21HISHISHISHIS(chain B and (resid 1 through 8 or (resid 9...BB08
31METMETVALVAL(chain C and (resid 1 through 97 or resid 99...CC1 - 979 - 105
32LYSLYSALAALA(chain C and (resid 1 through 97 or resid 99...CC99 - 148107 - 156
33LYSLYSVALVAL(chain C and (resid 1 through 97 or resid 99...CC150 - 97158 - 105
34METMETLEULEU(chain C and (resid 1 through 97 or resid 99...CC1 - 5789 - 586
35PHEPHELYSLYS(chain C and (resid 1 through 97 or resid 99...CC295 - 305303 - 313
36ASPASPASPASP(chain C and (resid 1 through 97 or resid 99...CC306314
37METMETLEULEU(chain C and (resid 1 through 97 or resid 99...CC1 - 5789 - 586
38METMETLEULEU(chain C and (resid 1 through 97 or resid 99...CC1 - 5789 - 586
39METMETLEULEU(chain C and (resid 1 through 97 or resid 99...CC1 - 5789 - 586
310METMETLEULEU(chain C and (resid 1 through 97 or resid 99...CC1 - 5789 - 586

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Components

#1: Protein Aspartate--tRNA ligase / Aspartyl-tRNA synthetase / AspRS


Mass: 67634.805 Da / Num. of mol.: 3 / Fragment: ElmeA.00145.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis (bacteria) / Gene: aspS, AYC66_05975, BAY09_04240, BAY10_00500 / Plasmid: ElmeA.00145.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A1T3DDI2, aspartate-tRNA ligase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1038 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Anatrace/Microlytic MGSG1 screen, condition C8: 25% (w/V) PEG 4000, 200mM Ammonium sulfate, 100mM sodium citrate tribasic / HCl pH 5.6: ElmeA.00145.a.B1.PW38328 at 22.48mg/ml: tray: 295094c8: ...Details: Anatrace/Microlytic MGSG1 screen, condition C8: 25% (w/V) PEG 4000, 200mM Ammonium sulfate, 100mM sodium citrate tribasic / HCl pH 5.6: ElmeA.00145.a.B1.PW38328 at 22.48mg/ml: tray: 295094c8: cryo: 15% EG, puck tcq3-6. Subunit C has few crystal lattice contactsleading to poor electron density.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 18, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→36.07 Å / Num. obs: 120694 / % possible obs: 98.5 % / Redundancy: 3.855 % / Biso Wilson estimate: 44.505 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.061 / Χ2: 1.023 / Net I/σ(I): 16.86 / Num. measured all: 465254 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.213.8150.5752.3733633904088150.7910.66997.5
2.21-2.273.9120.4713.0433736878686230.8690.54598.1
2.27-2.333.9140.3763.833019860184370.9090.43598.1
2.33-2.43.9120.3094.5231819826681340.9390.35798.4
2.4-2.483.9140.2455.5731149809879590.9580.28498.3
2.48-2.573.910.1976.9229930777276550.9720.22898.5
2.57-2.673.9030.1538.7129039754874400.9830.17798.6
2.67-2.783.9020.12710.3127799722971250.9870.14898.6
2.78-2.93.8960.09913.0326744696568650.9920.11598.6
2.9-3.043.8740.07816.425435665365650.9950.0998.7
3.04-3.213.860.05820.7324174633462620.9970.06898.9
3.21-3.43.8410.04625.3422763599859270.9980.05398.8
3.4-3.633.8230.03630.6821296563255700.9980.04298.9
3.63-3.933.7860.03135.0719746527352160.9990.03698.9
3.93-4.33.770.02839.2918019483747800.9990.03298.8
4.3-4.813.7690.02542.8516258436143140.9990.02998.9
4.81-5.553.7510.02542.1214477388938600.9990.02999.3
5.55-6.83.7450.02541.7412172329032500.9990.02998.8
6.8-9.623.70.02146.029353255925280.9990.02598.8
9.62-36.073.4280.0247.554693144513690.9990.02394.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18rc7 3834refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g51A as per MorDA

Resolution: 2.15→36.07 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 2019 1.67 %0
Rwork0.1871 ---
obs0.1878 120658 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 235.01 Å2 / Biso mean: 54.8857 Å2 / Biso min: 22.13 Å2
Refinement stepCycle: final / Resolution: 2.15→36.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13151 0 10 1049 14210
Biso mean--69.98 47.87 -
Num. residues----1715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813489
X-RAY DIFFRACTIONf_angle_d0.87718284
X-RAY DIFFRACTIONf_dihedral_angle_d19.9964892
X-RAY DIFFRACTIONf_chiral_restr0.0551991
X-RAY DIFFRACTIONf_plane_restr0.0062440
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6956X-RAY DIFFRACTION8.99TORSIONAL
12B6956X-RAY DIFFRACTION8.99TORSIONAL
13C6956X-RAY DIFFRACTION8.99TORSIONAL
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 (%)
2.15-2.20.29391450.24218363850898
2.2-2.260.28111240.23558441856598
2.26-2.330.27831530.22598395854898
2.33-2.410.29891540.21428386854098
2.41-2.490.26561340.21418430856498
2.49-2.590.23891320.20428476860898
2.59-2.710.26111410.20098425856699
2.71-2.850.26111250.21058514863999
2.85-3.030.26351550.20978471862699
3.03-3.260.24881560.19978485864199
3.26-3.590.21941500.18648524867499
3.59-4.110.20231480.16638535868399
4.11-5.180.18241480.1518557870599
5.18-36.070.19781540.17878637879198
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)
10.9045-0.06020.09970.73720.02290.9534-0.0048-0.0396-0.0170.0328-0.01090.0948-0.0364-0.254600.25270.02120.00710.30580.01850.318818.61159.7923-8.9526
20.3344-0.2310.23360.60110.16111.0212-0.07320.0332-0.0321-0.08390.0734-0.06070.0580.038900.3018-0.01880.02180.23620.00580.288650.2061-2.7085-30.9162
30.2896-0.16350.23210.1566-0.18060.770.03410.03960.0072-0.0556-0.0327-0.0261-0.0149-0.098100.309-0.03020.02850.2934-0.01160.321743.073.4566-52.1592
41.3245-0.3832-0.13421.27680.0440.7774-0.1539-0.0105-0.1987-0.04170.1009-0.08340.12990.1771-00.33470.04260.07150.285-0.02580.410966.4807-29.7756-33.3357
50.1581-0.3052-0.13510.2225-0.18680.7054-0.0332-0.08610.00640.02810.02280.0077-0.07910.0333-00.28610.0013-0.01070.2837-0.00760.293149.90643.3444-17.5455
60.215-0.28580.24130.3594-0.07580.8028-0.0827-0.07920.03450.1230.1016-0.0214-0.01910.0366-00.29870.0148-0.01050.31080.00480.324947.135-2.2284-8.7541
70.3281-0.74660.47481.91-0.9720.584-0.12710.00820.16090.3544-0.0589-0.3162-0.20250.0157-0.00080.39510.0381-0.05870.30780.00630.382159.9654-3.368213.5827
80.3185-0.0066-0.55890.95160.12840.6315-0.0731-0.13790.04930.09840.0625-0.1932-0.03460.22350.00010.2455-0.0302-0.05240.3335-0.02660.307456.83487.0565-15.6218
90.01130.0114-0.299-0.2797-0.19520.15110.3926-0.2681-0.0709-0.1298-0.01130.49920.3038-0.36160.00220.8627-0.2618-0.11381.30890.12090.770782.986210.569858.6992
100.5184-0.14150.59391.0989-0.55681.65591.2050.3758-0.2785-0.4044-0.58280.2668-0.21181.01150.36820.56450.2379-0.12681.0316-0.08580.3697111.778719.922335.494
112.0789-0.87382.92490.9871-0.0532.06060.9059-0.3763-0.2987-0.0902-0.10220.02710.9635-0.09170.53680.5467-0.0661-0.18990.6139-0.02770.338986.099518.97679.8708
121.14240.03731.79630.6514-0.88971.27930.37830.52860.012-0.1281-0.0655-0.3204-0.03880.04080.06680.61820.0608-0.06571.1139-0.0210.5324109.823723.995828.5605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 134 )A0 - 134
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 263 )A135 - 263
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 582 )A264 - 582
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 134 )B0 - 134
5X-RAY DIFFRACTION5chain 'B' and (resid 135 through 206 )B135 - 206
6X-RAY DIFFRACTION6chain 'B' and (resid 207 through 263 )B207 - 263
7X-RAY DIFFRACTION7chain 'B' and (resid 264 through 503 )B264 - 503
8X-RAY DIFFRACTION8chain 'B' and (resid 504 through 582 )B504 - 582
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 157 )C1 - 157
10X-RAY DIFFRACTION10chain 'C' and (resid 158 through 263 )C158 - 263
11X-RAY DIFFRACTION11chain 'C' and (resid 264 through 443 )C264 - 443
12X-RAY DIFFRACTION12chain 'C' and (resid 444 through 578 )C444 - 578

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