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- PDB-4e51: Crystal structure of a histidyl-tRNA synthetase HisRS from Burkho... -

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Basic information

Entry
Database: PDB / ID: 4.0E+51
TitleCrystal structure of a histidyl-tRNA synthetase HisRS from Burkholderia thailandensis bound to histidine
ComponentsHistidine--tRNA ligase
KeywordsLIGASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / aminoacylation / tRNA activation / charged tRNA / histidyl-adenylate / ATP-dependent / tRNA synthetase / aaRS
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Histidyl-anticodon-binding / 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 ...Histidyl-anticodon-binding / 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 speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Sci Rep / Year: 2017
Title: Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms.
Authors: Moen, S.O. / Edwards, T.E. / Dranow, D.M. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Sharma, A. / Manoil, C. / Staker, B.L. / Myler, P.J. / Lorimer, D.D.
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Sep 13, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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: Histidine--tRNA ligase
B: Histidine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1884
Polymers103,8752
Non-polymers3122
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-31 kcal/mol
Surface area34410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.160, 116.360, 142.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 9 - 501 / Label seq-ID: 30

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - D

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Components

#1: Protein Histidine--tRNA ligase / Histidyl-tRNA synthetase / HisRS


Mass: 51937.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I2235, hisS / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SWE3, histidine-tRNA ligase
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ButhA.00063.a.A1 PS01164 at 31 mg/mL with 5 mM L-histidine against Wizard III A3 focus screen, 350 mM magnesium formate, 12% PEG 3350 with 20% glycerol as cryo-protectant, crystal tracking ...Details: ButhA.00063.a.A1 PS01164 at 31 mg/mL with 5 mM L-histidine against Wizard III A3 focus screen, 350 mM magnesium formate, 12% PEG 3350 with 20% glycerol as cryo-protectant, crystal tracking ID 230808g3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 34582 / Num. obs: 34582 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 56.022 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.34
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.65-2.720.5244.22191822541199.9
2.72-2.790.4225.26191202446199.4
2.79-2.870.3316.65188842375199.8
2.87-2.960.2478.73188332343199.7
2.96-3.060.20210.65184502268199.9
3.06-3.170.1712.36180002185199.8
3.17-3.290.1316.06174432107199.7
3.29-3.420.10419.44167212042199.9
3.42-3.570.07525.57159701960199.8
3.57-3.750.06529.14152111884199.9
3.75-3.950.05633.03142021792199.8
3.95-4.190.04637.6132121702199.8
4.19-4.480.0442.35122221602199.8
4.48-4.840.03645.86113111493199.6
4.84-5.30.03546.87104441386199.6
5.3-5.930.03645.2594111262199.8
5.93-6.840.03545.581791124199.9
6.84-8.380.02953.8572059561100
8.38-11.850.02661.545280766199.9
11.85-500.02759.642178348176.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å19.61 Å
Translation2.6 Å19.61 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HTT

1htt


Resolution: 2.65→19.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2221 / WRfactor Rwork: 0.1875 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8262 / SU B: 21.915 / SU ML: 0.214 / SU R Cruickshank DPI: 0.4772 / SU Rfree: 0.2805 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.477 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1742 5 %RANDOM
Rwork0.206 ---
obs0.2078 34582 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.15 Å2 / Biso mean: 51.8046 Å2 / Biso min: 24.07 Å2
Baniso -1Baniso -2Baniso -3
1--3.91 Å20 Å20 Å2
2--5.78 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 22 64 6127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196182
X-RAY DIFFRACTIONr_bond_other_d0.0040.023941
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9538419
X-RAY DIFFRACTIONr_angle_other_deg1.1339602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25824.207271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45315899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2471535
X-RAY DIFFRACTIONr_chiral_restr0.0750.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217060
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021263
Refine LS restraints NCS

Ens-ID: 1 / Number: 11800 / Refine-ID: X-RAY DIFFRACTION / Type: RESTRAINTS / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 129 -
Rwork0.33 2212 -
all-2341 -
obs--99.7 %
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)
10.11550.16660.05070.608-0.29840.42910.05810.0087-0.00970.018-0.05980.02360.03760.1150.00170.120.0441-0.03060.14740.01550.10125.27050.354744.3262
20.14970.1759-0.13580.5943-0.39260.3406-0.0325-0.11860.0678-0.0255-0.0010.0068-0.04210.08450.03350.0825-0.0135-0.02070.1883-0.03480.1488.476719.574236.0078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 439
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B8 - 439
4X-RAY DIFFRACTION2B501

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