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- PDB-3ziu: Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase wit... -

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Basic information

Entry
Database: PDB / ID: 3ziu
TitleCrystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site
ComponentsLEUCYL-TRNA SYNTHETASE
KeywordsLIGASE
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-(L-leucylsulfamoyl)adenosine / leucine--tRNA ligase
Similarity search - Component
Biological speciesMYCOPLASMA MOBILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLi, L. / Palencia, A. / Lukk, T. / Li, Z. / Luthey-Schulten, Z.A. / Cusack, S. / Martinis, S.A. / Boniecki, M.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Leucyl-tRNA Synthetase Editing Domain Functions as a Molecular Rheostat to Control Codon Ambiguity in Mycoplasma Pathogens.
Authors: Li, L. / Palencia, A. / Lukk, T. / Li, Z. / Luthey-Schulten, Z.A. / Cusack, S. / Martinis, S.A. / Boniecki, M.T.
History
DepositionJan 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: LEUCYL-TRNA SYNTHETASE
B: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,09014
Polymers150,2512
Non-polymers1,84012
Water18,2311012
1
A: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0457
Polymers75,1251
Non-polymers9206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0457
Polymers75,1251
Non-polymers9206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.851, 202.851, 213.922
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 LEUCYL-TRNA SYNTHETASE


Mass: 75125.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 5-O-N-LEUCYL-SULFAMOYLADENOSINE, LEUCYL ADENYLATE ANALOGUE (LEUAMS) BOUND TO THE ACTIVE SITE
Source: (gene. exp.) MYCOPLASMA MOBILE (bacteria) / Plasmid: P14LIMMOLEURS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q6KHA5, leucine-tRNA ligase
#2: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / 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: 2.82 Å3/Da / Density % sol: 56.46 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1M BIS-TRIS PH 5.5 0.6M AMMONIUM ACETATE 20% V/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.07→12 Å / Num. obs: 101516 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 18.45
Reflection shellResolution: 2.07→2.12 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.56 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AQ7

4aq7


Resolution: 2.07→135.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.485 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19893 5079 5 %RANDOM
Rwork0.1596 ---
obs0.16155 96445 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.711 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0.6 Å20 Å2
2---1.2 Å20 Å2
3---1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.07→135.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9929 0 122 1012 11063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0210409
X-RAY DIFFRACTIONr_bond_other_d0.0010.027257
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.96314085
X-RAY DIFFRACTIONr_angle_other_deg0.913317725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04451215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78524.859498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.572151900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7681537
X-RAY DIFFRACTIONr_chiral_restr0.090.21481
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022120
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.071→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 337 -
Rwork0.255 6873 -
obs--99.2 %

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