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- PDB-3lss: Trypanosoma brucei seryl-tRNA synthetase in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 3lss
TitleTrypanosoma brucei seryl-tRNA synthetase in complex with ATP
ComponentsSeryl-tRNA synthetase
KeywordsLIGASE / aminoacyl-tRNA synthetase / tRNA ligase / AARS / SerRS / translation / ATP-binding / nucleotide-binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / cilium / tRNA binding / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / MALONATE ION / serine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: to be published
Title: X-ray crystal structure of Seryl-tRNA synthetase from the eukaryotic parasite Trypanosoma brucei.
Authors: Larson, E.T. / Zhang, L. / Napuli, A. / Mueller, N. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Hol, W.G.J. / Merritt, E.A.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seryl-tRNA synthetase
B: Seryl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9477
Polymers108,7052
Non-polymers1,2415
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-45 kcal/mol
Surface area38720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.652, 175.652, 248.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Seryl-tRNA synthetase


Mass: 54352.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: SerRS, Tb11.02.5020 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q384V4, serine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.39 Å3/Da / Density % sol: 63.76 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 7
Details: 1 ul 11 mg/ml protein in SGPP buffer mixed with 0.5 ul 2.4 M sodium malonate; crystal then soaked in 3.4 M sodium malonate (pH 7.0) supplemented with 10 mM ATP for 25 minutes before freezing. ...Details: 1 ul 11 mg/ml protein in SGPP buffer mixed with 0.5 ul 2.4 M sodium malonate; crystal then soaked in 3.4 M sodium malonate (pH 7.0) supplemented with 10 mM ATP for 25 minutes before freezing., sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2008
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 106754 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 8 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.025 / Net I/σ(I): 9.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.5 / Num. unique all: 10577 / Χ2: 1.004 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3LSQ

3lsq


Resolution: 1.95→34.57 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.944 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.195 5392 5.1 %RANDOM
Rwork0.168 ---
obs0.169 106719 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 154.12 Å2 / Biso mean: 50.159 Å2 / Biso min: 25.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.57 Å20 Å2
2--1.14 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.95→34.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7265 0 77 341 7683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227466
X-RAY DIFFRACTIONr_bond_other_d0.0010.025188
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.97310073
X-RAY DIFFRACTIONr_angle_other_deg0.863312632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02524.25360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.065151391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5591559
X-RAY DIFFRACTIONr_chiral_restr0.0820.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021496
X-RAY DIFFRACTIONr_mcbond_it2.0744522
X-RAY DIFFRACTIONr_mcbond_other0.65941844
X-RAY DIFFRACTIONr_mcangle_it3.25267307
X-RAY DIFFRACTIONr_scbond_it3.8562944
X-RAY DIFFRACTIONr_scangle_it5.824102764
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 394 -
Rwork0.247 7382 -
all-7776 -
obs--99.45 %
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)
17.15210.4136.13450.18150.68856.74960.1312-0.1120.07150.11430.1451-0.0821-0.05770.6422-0.27630.2858-0.09070.04920.4172-0.12450.302240.219519.364288.5994
28.1862-3.96797.927.1661-7.35619.45340.10210.1413-0.94740.07220.4069-0.4421.7032.1998-0.5090.64040.1940.04151.0013-0.28430.322761.510618.679117.7332
39.45751.28533.89530.951.09334.691-0.3759-0.15250.9506-0.06010.0845-0.141-0.78170.60850.29150.311-0.08290.00760.2305-0.08260.303431.774125.237285.4568
40.7801-0.09590.46641.2524-0.05811.8548-0.0470.09080.0792-0.09760.0457-0.1633-0.13560.25240.00130.1352-0.00670.03360.06060.00160.13357.542536.409793.6043
53.512-1.9261-0.09486.3453-0.19541.34390.05770.08380.2425-0.2509-0.0473-0.2569-0.03190.3202-0.01030.1299-0.00240.01680.1377-0.02280.106617.976228.973100.0969
61.2382-0.27620.3370.61590.16551.0764-0.02420.06450.0088-0.03980.0282-0.1018-0.01330.1731-0.00410.14930.0049-0.00240.0428-0.00250.1212.881423.405688.1861
71.6515-0.7774-0.00392.1166-0.23691.8159-0.0115-0.08710.1495-0.06320.04170.022-0.0253-0.0358-0.03020.1204-0.02610.00330.0123-0.01280.04082.035629.17291.9819
83.05024.6835-4.26147.3696-6.24886.4750.0232-0.0162-0.1452-0.01170.0271-0.405-0.15750.1084-0.05030.8588-0.15260.17880.2536-0.02510.32167.076274.3879119.6893
91.7840.8062-0.91757.0896-2.09935.77890.0451-0.16460.08380.4951-0.17850.30980.0364-0.1050.13340.1353-0.08340.01570.0897-0.05190.144219.609195.216193.5642
105.26844.0918-4.9756.6105-4.22046.97010.27-0.5363-0.31560.1487-0.536-0.8535-0.39731.08180.2660.664-0.02480.01590.2816-0.00230.23847.98665.2943121.4505
110.9808-0.1742-0.04671.1736-0.1661.817-0.05-0.17420.04980.20280.0876-0.1342-0.1930.1825-0.03760.17460.02-0.00290.0847-0.00820.11195.396238.7461114.0043
122.9966-2.68850.46766.3688-1.49021.9036-0.2499-0.24080.09150.44750.2346-0.3041-0.39390.11630.01530.2243-0.0102-0.00240.0726-0.03340.09575.792349.2714108.7515
130.27620.4281-0.39381.6115-1.95842.61060.0101-0.03470.04530.43690.03840.0289-0.5344-0.0406-0.04850.30430.07170.03370.08590.02750.1332-5.068951.7208117.7346
141.371-0.81920.45372.0084-0.6222.4737-0.092-0.0964-0.14950.23320.1829-0.1092-0.0615-0.0883-0.09090.12720.05470.03150.07450.01570.0666-3.389436.9754114.9035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 48
2X-RAY DIFFRACTION2A49 - 119
3X-RAY DIFFRACTION3A120 - 156
4X-RAY DIFFRACTION4A157 - 253
5X-RAY DIFFRACTION5A254 - 305
6X-RAY DIFFRACTION6A306 - 404
7X-RAY DIFFRACTION7A405 - 467
8X-RAY DIFFRACTION8B-2 - 46
9X-RAY DIFFRACTION9B47 - 120
10X-RAY DIFFRACTION10B121 - 153
11X-RAY DIFFRACTION11B154 - 253
12X-RAY DIFFRACTION12B254 - 314
13X-RAY DIFFRACTION13B315 - 409
14X-RAY DIFFRACTION14B410 - 465

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