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- PDB-3hrk: Histidyl-tRNA synthetase from Trypanosoma cruzi (Histidyl-adenyla... -

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Basic information

Entry
Database: PDB / ID: 3hrk
TitleHistidyl-tRNA synthetase from Trypanosoma cruzi (Histidyl-adenylate 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
HISTIDYL-ADENOSINE MONOPHOSPHATE / histidine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsArakaki, T.L. / Merritt, 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
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 / 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
B: Histidyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3755
Polymers102,3712
Non-polymers1,0043
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-35 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.360, 166.987, 66.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 70
2112B1 - 70
1122A76 - 450
2122B76 - 450

NCS ensembles :
ID
1
2

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Components

#1: Protein Histidyl-tRNA synthetase


Mass: 51185.590 Da / Num. of mol.: 2 / 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-HAM / HISTIDYL-ADENOSINE MONOPHOSPHATE


Mass: 484.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N8O8P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 M Lithium Sulfate, 28% PEG 3350, 0.1 M Bis/Tris pH 5.5, 1mM TCEP, 10 mM L-Histidine; subsequent soak against effective concentration 5mM ATP, 5mM MgCl2, 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: Apr 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 19599 / % possible obs: 80.3 % / Redundancy: 3 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.12 / Χ2: 1.071 / Net I/σ(I): 7.746
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.05-3.162.70.90516411.019168.7
3.16-3.292.80.62617391.08172.8
3.29-3.432.80.48817411.176172.3
3.43-3.622.70.35817881.176174.6
3.62-3.842.70.25218601.25177.3
3.84-4.142.70.19419611.127180.6
4.14-4.562.80.11221351.072187.8
4.56-5.213.10.09122251.065190.7
5.21-6.573.60.08822531.015190.6
6.57-503.60.05122560.904186

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.04 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.04 Å42.56 Å
Translation3.04 Å42.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HRJ

3hrj
PDB Unreleased entry


Resolution: 3.05→42.56 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.822 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.736 / SU B: 54.71 / SU ML: 0.506 / SU R Cruickshank DPI: 0.464 / SU Rfree: 0.612 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.612 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1022 5.2 %RANDOM
Rwork0.232 ---
obs0.236 19569 80.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.5 Å2 / Biso mean: 29.905 Å2 / Biso min: 3.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--5.67 Å20 Å2
3----4.74 Å2
Refinement stepCycle: LAST / Resolution: 3.05→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6477 0 67 0 6544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226728
X-RAY DIFFRACTIONr_bond_other_d0.0010.024583
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.989149
X-RAY DIFFRACTIONr_angle_other_deg0.8033.00111075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03623.158304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.497151111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1111560
X-RAY DIFFRACTIONr_chiral_restr0.0560.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021407
X-RAY DIFFRACTIONr_mcbond_it0.3631.54155
X-RAY DIFFRACTIONr_mcbond_other0.0451.51683
X-RAY DIFFRACTIONr_mcangle_it0.6926700
X-RAY DIFFRACTIONr_scbond_it0.82432573
X-RAY DIFFRACTIONr_scangle_it1.4884.52442
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1129TIGHT POSITIONAL0.020.05
1197MEDIUM POSITIONAL0.020.5
1129TIGHT THERMAL0.9210
1197MEDIUM THERMAL0.9610
22191TIGHT POSITIONAL0.020.05
22699MEDIUM POSITIONAL0.020.5
22191TIGHT THERMAL1.7210
22699MEDIUM THERMAL1.8210
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.615 44 -
Rwork0.37 1101 -
all-1145 -
obs--64.43 %
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)
12.70941.29151.76914.39911.37830.81820.3674-0.42380.21340.9187-0.54870.84630.31-0.25850.18130.4842-0.19150.23680.2721-0.16030.254815.25526.34719.288
26.79023.65380.26395.7078-0.74461.83890.7397-1.2386-0.58611.3417-0.6702-0.39960.51140.1161-0.06950.7104-0.166-0.09860.33390.05940.182834.55229.19728.721
30.8719-0.4259-0.852.6388-0.24316.52630.302-0.51930.12480.3624-0.31150.0530.0474-0.2570.00960.3321-0.32340.07510.5865-0.09190.288629.86843.51736.101
42.09671.12211.06591.82141.26112.81640.337-0.65790.21510.4135-0.45250.13890.0899-0.45540.11560.1821-0.10570.13480.2415-0.02110.255324.65540.35223.105
55.81023.5983.46665.7874-2.75819.186-0.02070.2242-0.28870.1533-0.0949-0.72971.06180.45360.11560.3370.1004-0.09440.06190.00010.394740.70825.07618.411
66.47872.44393.03271.46020.01098.14951.1745-0.4257-1.50730.56-0.6146-0.30541.2091-0.1809-0.55990.5989-0.2606-0.05660.3711-0.07590.597821.2515.6116.716
74.26061.1131-0.57164.3281.18823.42140.3181-0.2107-1.19890.6133-0.1361-0.58430.76120.3317-0.1820.45750.055-0.14410.11590.02180.473826.6935.8014.295
81.90551.74110.523.96221.30991.46250.08220.0109-0.60990.18650.0128-0.56110.41360.1546-0.09490.21520.08570.0280.04340.01590.276331.44919.1845.137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 70
2X-RAY DIFFRACTION2A71 - 161
3X-RAY DIFFRACTION3A162 - 247
4X-RAY DIFFRACTION4A248 - 435
5X-RAY DIFFRACTION5B6 - 70
6X-RAY DIFFRACTION6B71 - 158
7X-RAY DIFFRACTION7B159 - 247
8X-RAY DIFFRACTION8B248 - 435

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