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- PDB-6od8: Crystal structure of a putative aspartyl-tRNA synthetase from Lei... -

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Basic information

Entry
Database: PDB / ID: 6od8
TitleCrystal structure of a putative aspartyl-tRNA synthetase from Leishmania major Friedlin
ComponentsPutative aspartyl-tRNA synthetase
KeywordsLIGASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / 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
FORMIC ACID / Aspartyl-tRNA synthetase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a putative aspartyl-tRNA synthetase from Leishmania major Friedlin
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative aspartyl-tRNA synthetase
B: Putative aspartyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,13321
Polymers126,9852
Non-polymers1,14719
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-0 kcal/mol
Surface area38700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.010, 142.360, 68.280
Angle α, β, γ (deg.)90.000, 97.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative aspartyl-tRNA synthetase


Mass: 63492.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_30_0460 / Plasmid: LemaA.00612.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q4Q7R2, aspartate-tRNA ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG-1 screen G9: 20% (w/V) PEG 3350, 200mM sodium formate: LemaA.00612.a.B1.PW38547 at 21.8mg/ml: cryo: 20% EG in two steps: tray 306454 G9: puck xyn7-2. For experimental ...Details: Microlytic MCSG-1 screen G9: 20% (w/V) PEG 3350, 200mM sodium formate: LemaA.00612.a.B1.PW38547 at 21.8mg/ml: cryo: 20% EG in two steps: tray 306454 G9: puck xyn7-2. For experimental phasing, a crystal from the same well was incubated for 10sec each in a solution of a) 90% reservoir and 10% 2.5M Sodium iodide in ethylene glycol and a solution of b) a) 80% reservoir and 20% 2.5M Sodium iodide in ethylene glycol a s and vitrified: puck: bbh6-4. Well diffracting monoclinic crystals with a larger unit cell and four copies of the protein in the ASU also grew under condition MCSG-1 D9: 25% (w/V) PEG 3350, 200mM NaCl, 100mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→46.111 Å / Num. obs: 97249 / % possible obs: 99 % / Redundancy: 8.76 % / Biso Wilson estimate: 29.613 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.064 / Χ2: 1.063 / Net I/σ(I): 20.88 / Num. measured all: 851909 / Scaling rejects: 572
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.93.1090.3342.8766610.8720.492.1
1.9-1.954.3980.2944.268470.9320.33396.8
1.95-2.015.980.2376.467490.9650.2698.5
2.01-2.076.7410.1888.5966600.9810.20499.5
2.07-2.147.5780.16110.6964510.9880.173100
2.14-2.218.3160.13713.4662720.9920.14699.9
2.21-2.298.920.12215.7960210.9940.13100
2.29-2.3910.0720.11518.2557920.9950.121100
2.39-2.4911.050.10620.4156110.9970.111100
2.49-2.6211.0380.09722.2853340.9970.102100
2.62-2.7611.0550.08624.8450820.9970.091100
2.76-2.9311.0230.07727.947960.9980.0899.8
2.93-3.1311.0330.06731.8845230.9980.07100
3.13-3.3810.8920.05836.2341960.9990.06199.9
3.38-3.710.7910.05141.2638590.9990.05499.8
3.7-4.1410.7110.04545.1735030.9990.04899.8
4.14-4.7810.7820.04147.3731100.9990.043100
4.78-5.8511.1180.0446.5426120.9990.04299.8
5.85-8.2711.3160.03846.520430.9990.039100
8.27-46.11110.970.03151.1511270.9990.03299.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.15rc1_3423)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→46.111 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.47
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 1892 1.95 %0
Rwork0.1567 ---
obs0.1574 97236 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.8 Å2 / Biso mean: 29.6474 Å2 / Biso min: 8.9 Å2
Refinement stepCycle: final / Resolution: 1.85→46.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7927 0 77 820 8824
Biso mean--44.23 37.46 -
Num. residues----1011
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 (%)
1.85-1.89630.26841280.23156303643192
1.8963-1.94750.26381280.20446614674297
1.9475-2.00480.21461410.17916738687998
2.0048-2.06960.23881390.175468336972100
2.0696-2.14350.23051360.168368536989100
2.1435-2.22930.23031320.167768496981100
2.2293-2.33080.19831380.162668907028100
2.3308-2.45370.20931300.159568957025100
2.4537-2.60740.20611360.16568446980100
2.6074-2.80870.18921310.166968747005100
2.8087-3.09130.22081410.162169127053100
3.0913-3.53850.15511280.149968767004100
3.5385-4.45750.15371390.125569097048100
4.4575-46.12550.17521450.147369547099100
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)
12.40640.12960.21961.8024-0.46521.5941-0.0455-0.2348-0.47340.07240.23980.35520.1095-0.3576-0.1490.1888-0.0206-0.03790.21460.06090.3762-52.2792-20.8661-25.9006
20.76560.09460.41890.72480.1310.750.0462-0.0743-0.09690.1394-0.0297-0.1380.04970.0611-0.00310.1433-0.01-0.00180.16220.03380.1352-14.99521.8697-12.295
30.31750.1015-0.09670.0433-0.00130.1193-0.19110.00290.32560.39650.0509-0.2388-0.37090.03440.06920.4488-0.0623-0.18560.2660.01420.4013-5.825232.5201-5.4918
41.4810.1363-0.69292.3105-0.22732.2218-0.102-0.07150.30950.31860.1345-0.0901-0.5581-0.156-0.02880.37960.0017-0.06310.18170.02580.2778-14.651440.8896-15.0668
50.78520.34290.19991.1515-0.01830.5671-0.04710.12830.0453-0.08630.0289-0.0973-0.08980.06860.0150.1213-0.00530.01450.14850.01940.1098-21.0511.8367-30.9789
60.88670.13830.23290.6296-0.15830.5594-0.01720.19410.0636-0.17960.0370.0915-0.0058-0.0312-0.0280.1475-0.0113-0.00420.18370.03320.1205-38.70457.5939-42.8057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 180 )A39 - 180
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 550 )A181 - 550
3X-RAY DIFFRACTION3chain 'B' and (resid 35 through 70 )B35 - 70
4X-RAY DIFFRACTION4chain 'B' and (resid 71 through 155 )B71 - 155
5X-RAY DIFFRACTION5chain 'B' and (resid 156 through 301 )B156 - 301
6X-RAY DIFFRACTION6chain 'B' and (resid 302 through 550 )B302 - 550

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