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- PDB-3lc0: Histidyl-tRNA synthetase from Trypanosoma cruzi (Histidine complex) -

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Basic information

Entry
Database: PDB / ID: 3lc0
TitleHistidyl-tRNA synthetase from Trypanosoma cruzi (Histidine complex)
ComponentsHistidyl-tRNA synthetase
KeywordsLIGASE / tRNA-ligase / Aminoacyl-tRNA synthetase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / histidine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / previous isomorphous structure / Resolution: 1.8 Å
AuthorsMerritt, E.A. / Larson, E.T. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of Trypanosomal Histidyl-tRNA Synthetase Illuminate Differences between Eukaryotic and Prokaryotic Homologs.
Authors: Merritt, E.A. / Arakaki, T.L. / Gillespie, J.R. / Larson, E.T. / Kelley, A. / Mueller, N. / Napuli, A.J. / Kim, J. / Zhang, L. / Verlinde, C.L. / Fan, E. / Zucker, F. / Buckner, F.S. / Van ...Authors: Merritt, E.A. / Arakaki, T.L. / Gillespie, J.R. / Larson, E.T. / Kelley, A. / Mueller, N. / Napuli, A.J. / Kim, J. / Zhang, L. / Verlinde, C.L. / Fan, E. / Zucker, F. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJan 19, 2010ID: 3HRJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3422
Polymers51,1861
Non-polymers1561
Water3,207178
1
A: Histidyl-tRNA synthetase
hetero molecules

A: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6844
Polymers102,3712
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7600 Å2
ΔGint-33 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.030, 118.840, 65.980
Angle α, β, γ (deg.)90.00, 132.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histidyl-tRNA synthetase


Mass: 51185.590 Da / Num. of mol.: 1 / Fragment: UNP residues 45-478
Source method: isolated from a genetically manipulated source
Details: uncleaved / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053507019.40 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DA54, histidine-tRNA ligase
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 M Lithium Sulfate, 26% PEG 3350, 0.1 M Bis/Tris pH 5.5, 1mM TCEP, 10 mM L-Histidine, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97923 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.8→48 Å / Num. all: 47130 / Num. obs: 47130 / % possible obs: 99.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.78 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.0065
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.8-1.93.750.64256856847199.85
1.9-2.013.750.34244846521199.95
2.01-2.153.760.2229666108199.99
2.15-2.323.770.132151657041100
2.32-2.553.790.081987852411100
2.55-2.853.80.061804247421100
2.85-3.293.820.051597441821100
3.29-4.023.820.031355035501100
4.02-5.693.820.03105442763199.96
5.69-483.680.0254101472196.36

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9data scaling
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: previous isomorphous structure
Resolution: 1.8→34.108 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.119 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2112 2374 5.038 %
Rwork0.1926 --
obs-47123 99.822 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.857 Å2
Baniso -1Baniso -2Baniso -3
1-1.671 Å20 Å21.391 Å2
2---0.948 Å20 Å2
3---1.159 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 11 178 3437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223384
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9664600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72423.247154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60315572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7891529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212584
X-RAY DIFFRACTIONr_mcbond_it0.6111.52098
X-RAY DIFFRACTIONr_mcangle_it1.13723387
X-RAY DIFFRACTIONr_scbond_it1.85631286
X-RAY DIFFRACTIONr_scangle_it3.1144.51207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.3561610.3283295346599.74
1.847-1.8970.3191720.2873203338299.793
1.897-1.9520.2921710.2483117329199.909
1.952-2.0120.2241760.2163037321699.907
2.012-2.0770.2461290.2112993312399.968
2.077-2.150.2291430.2042824296899.966
2.15-2.2310.2141470.1972748289699.965
2.231-2.3220.2321250.1926612786100
2.322-2.4240.2131260.19825502676100
2.424-2.5420.2071430.1942425256999.961
2.542-2.6790.2151170.20323092426100
2.679-2.840.2311070.21522142321100
2.84-3.0350.2331130.20220452158100
3.035-3.2760.2161000.19319182018100
3.276-3.5850.195920.1791781187499.947
3.585-4.0030.173980.17815821680100
4.003-4.6110.171870.1514051492100
4.611-5.6220.181770.1681206128599.844
5.622-7.8450.267580.198931989100
7.845-34.1080.198320.19250559290.709
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)
10.40.33470.3390.4914-0.40253.16-0.0273-0.0024-0.0757-0.0017-0.0836-0.11840.35910.37810.11090.20250.05580.03180.22340.0190.28836.2362.371-1.512
20.3375-2.0838-2.38811.96193.03035.0857-0.05670.1133-0.44790.1678-0.14610.33810.4198-0.02910.20280.4705-0.03230.04020.0798-0.10970.47170.745-15.822-14.583
30.9256-0.0136-0.10431.513-0.05782.6437-0.04560.0331-0.13770.0621-0.00860.09850.4648-0.0260.05420.2735-0.0120.02920.1787-0.01450.2765-1.8-1.605-13.229
41.1032-0.428-0.51171.17740.11292.399-0.11890.2884-0.2892-0.3756-0.10640.11130.4494-0.0450.22530.26380.00290.05170.2691-0.08260.22987.228-4.482-30.24
57.6067-0.0449-1.379218.9347-4.85152.8033-0.43911.526-0.9803-1.30640.1589-1.57990.2128-0.17890.28020.4528-0.0530.28250.3494-0.3010.209812.191-9.315-37.255
61.50840.3761-0.1581.12410.22921.7261-0.01530.1045-0.0443-0.1057-0.00340.00350.15280.19530.01870.21520.00930.0280.2457-0.00550.25576.8693.365-22.43
72.63150.4517-0.22072.2882-0.48722.88110.0155-0.18440.16830.1927-0.0669-0.175-0.24960.20420.05140.21810.0009-0.06090.1989-0.04380.26939.07622.35223.927
811.3453-8.08679.419.09822.86217.3609-0.69080.56141.98180.42410.2534-0.2198-0.41020.57360.43740.2373-0.0191-0.04220.06350.07830.82876.69634.28122.453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA47 - 92
2X-RAY DIFFRACTION2ALLA93 - 112
3X-RAY DIFFRACTION3ALLA113 - 196
4X-RAY DIFFRACTION4ALLA197 - 237
5X-RAY DIFFRACTION5ALLA238 - 286
6X-RAY DIFFRACTION6ALLA287 - 379
7X-RAY DIFFRACTION7ALLA380 - 455
8X-RAY DIFFRACTION8ALLA468 - 477

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