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- PDB-5w25: Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 5w25
TitleCrystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed with L-Aspartic Acid
ComponentsAspartate--tRNA(Asp/Asn) ligase
KeywordsLIGASE / SSGCID / Aspartate--tRNA(Asp/Asn) ligase / ATP / L-aspartate / AspRS / tRNA aminoacylation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / cell wall / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
GAD-like domain / 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 ...GAD-like domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Gyrase A; domain 2 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / GLUTAMIC ACID / LYSINE / Aspartate--tRNA(Asp/Asn) ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed with L-Aspartic Acid
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: 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
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate--tRNA(Asp/Asn) ligase
B: Aspartate--tRNA(Asp/Asn) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8849
Polymers134,8822
Non-polymers1,0027
Water75742
1
A: Aspartate--tRNA(Asp/Asn) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0165
Polymers67,4411
Non-polymers5754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aspartate--tRNA(Asp/Asn) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8684
Polymers67,4411
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-36 kcal/mol
Surface area45870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.720, 158.240, 75.740
Angle α, β, γ (deg.)90.000, 93.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aspartate--tRNA(Asp/Asn) ligase / Aspartyl-tRNA synthetase / AspRS / Non-discriminating aspartyl-tRNA synthetase / ND-AspRS


Mass: 67440.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: aspS, Rv2572c, MTCY227.29 / Plasmid: MytuD.00145.b.M1 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WFW3, aspartate-tRNAAsn ligase
#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartyl-tRNA synthetase / AspRS / Non-discriminating aspartyl-tRNA synthetase / ND-AspRS / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H7NO4 / References: aspartate-tRNAAsn ligase
#3: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MytuD.00145.b.M1.PD00305 at 10.3 mg/ml was incubated with 1 mM L-aspartic acid, then mixed 1:1 with Morpheus (h1): 10% (w/v) PEG-20000, 20% (v/v) PEG MME 550, 0.1 M MES/imidazole, pH = 6.5, ...Details: MytuD.00145.b.M1.PD00305 at 10.3 mg/ml was incubated with 1 mM L-aspartic acid, then mixed 1:1 with Morpheus (h1): 10% (w/v) PEG-20000, 20% (v/v) PEG MME 550, 0.1 M MES/imidazole, pH = 6.5, 0.02 M each L-glutamate, DL-alanine, glycine, DL-lysine, DL-serine, Tray 251523h1, puck gdy9-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→43.254 Å / Num. obs: 44023 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.143 % / Biso Wilson estimate: 62.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.056 / Χ2: 1.064 / Net I/σ(I): 16.48 / Num. measured all: 182369 / Scaling rejects: 56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.724.2530.5172.5932730.9480.59299.7
2.72-2.794.2630.446331450.9570.5199.7
2.79-2.874.2680.3673.6930600.9670.41999.9
2.87-2.964.2760.2764.7530080.9820.31699.8
2.96-3.064.2570.2096.2628820.9880.239100
3.06-3.174.2390.1568.2228240.9910.17999.9
3.17-3.294.2330.11910.0627050.9960.13699.7
3.29-3.424.1930.08813.1626300.9970.10199.8
3.42-3.574.1210.07115.6124970.9980.08299.8
3.57-3.754.0990.05818.8723620.9980.06799.7
3.75-3.954.0950.04921.5122840.9990.05699.7
3.95-4.194.050.0425.3121470.9990.04699.7
4.19-4.484.0530.03330.0820190.9990.03999.7
4.48-4.843.9890.03232.518840.9990.03799.8
4.84-5.33.920.03133.4117330.9990.036100
5.3-5.933.8750.03233.4415800.9990.03799.8
5.93-6.843.8460.0335.8414000.9990.035100
6.84-8.384.0350.02440.7211670.9990.02899.9
8.38-11.854.0460.02143.379180.9990.02499.9
11.85-43.2543.8710.02143.235050.9990.02497.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RMF

4rmf


Resolution: 2.65→43.254 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.57
RfactorNum. reflection% reflection
Rfree0.245 1973 4.49 %
Rwork0.2247 --
obs0.2257 43910 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 247.45 Å2 / Biso mean: 102.3951 Å2 / Biso min: 37.41 Å2
Refinement stepCycle: final / Resolution: 2.65→43.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8225 0 50 42 8317
Biso mean--140.45 73.43 -
Num. residues----1151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028462
X-RAY DIFFRACTIONf_angle_d0.4611556
X-RAY DIFFRACTIONf_chiral_restr0.0571287
X-RAY DIFFRACTIONf_plane_restr0.0051567
X-RAY DIFFRACTIONf_dihedral_angle_d14.4784854
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 (%)
2.65-2.71620.39061730.36992940311399
2.7162-2.78960.38221330.33122978311199
2.7896-2.87170.34921120.316629973109100
2.8717-2.96440.31791400.31462991313199
2.9644-3.07030.35011200.290329923112100
3.0703-3.19320.33321300.27630233153100
3.1932-3.33850.29761370.272529733110100
3.3385-3.51440.31091380.247230103148100
3.5144-3.73450.27521370.233630013138100
3.7345-4.02260.23261460.222429983144100
4.0226-4.42710.1951450.190129753120100
4.4271-5.06680.20251650.184529973162100
5.0668-6.38040.24171550.215530193174100
6.3804-43.25950.19031420.181930433185100
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)
11.25311.2982-0.31034.99380.2190.68970.1107-0.0421-0.10420.7438-0.2405-0.10190.23310.01430.1450.4589-0.0075-0.0590.4847-0.03530.4243.4529-15.664.2238
21.21020.4165-0.42862.76680.96181.9073-0.19560.4389-0.1765-1.47720.1797-0.7581-0.071-0.0363-0.05090.9667-0.02690.25390.6615-0.02490.704414.4556-3.5011-23.7118
32.02062.02821.97472.03841.96752.0097-0.91990.0857-0.1913-0.22440.81940.95770.94340.82190.13661.38550.1536-0.9361.2193-0.00892.09822.215117.9204-0.9841
41.06130.289-0.23726.67150.07491.28260.241-0.09410.3640.8411-0.1416-0.0258-0.18670.0463-0.06250.4403-0-0.01540.5011-0.03320.4725.609615.38332.3748
51.3783-0.6694-0.61851.74860.07550.67040.1795-0.1842-0.03751.8834-0.22761.6750.1306-0.18810.47691.5798-0.22030.85330.7456-0.15591.26-17.8091.607320.6116
62228.0890.76471.99991.4242-4.29971.5876-3.27981.51881.5932-5.0898-0.1028-3.02371.66050.21550.14551.194-0.1612.18765.0116-18.141321.1613
78.4154-3.5501-6.9597222-0.5968-0.7753-0.7798-0.3291-0.1379-0.25571.68492.15380.72041.65380.6106-0.65671.49790.10551.943715.786917.15064.736
87.4938-2.2847-3.14012.03021.95922.0684-2.73973.8844-3.23871.88761.35260.55960.294-1.57311.41261.5170.14010.03281.935-0.1141.557613.8278-23.94657.4919
92-7.6991-1.914321.10986.2471.1353-1.3034-0.718-2.21040.81152.78342.24542.6957-1.93952.4009-0.1375-0.61221.61550.31442.016711.166823.470411.6767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 242 )A0 - 242
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 701 )A243 - 701
3X-RAY DIFFRACTION3chain 'A' and (resid 702 through 702 )A702
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 242 )B0 - 242
5X-RAY DIFFRACTION5chain 'B' and (resid 243 through 701 )B243 - 701
6X-RAY DIFFRACTION6chain 'B' and (resid 702 through 702 )B702
7X-RAY DIFFRACTION7chain 'A' and (resid 703 through 703 )A703
8X-RAY DIFFRACTION8chain 'A' and (resid 704 through 704 )A704
9X-RAY DIFFRACTION9chain 'B' and (resid 703 through 703 )B703

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