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- PDB-3pz6: The crystal structure of GlLeuRS-CP1 -

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Basic information

Entry
Database: PDB / ID: 3pz6
TitleThe crystal structure of GlLeuRS-CP1
ComponentsLeucyl-tRNA synthetase
KeywordsLIGASE / Editing domain / GlLeuRS_CP1
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding
Similarity search - Function
Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
leucine--tRNA ligase
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, R.J. / Du, D.H. / Wang, E.D.
CitationJournal: Biochem.J. / Year: 2011
Title: Peripheral insertion modulates the editing activity of the isolated CP1 domain of leucyl-tRNA synthetase
Authors: Liu, R.J. / Tan, M. / Du, D.H. / Xu, B.S. / Eriani, G. / Wang, E.D.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucyl-tRNA synthetase
B: Leucyl-tRNA synthetase
C: Leucyl-tRNA synthetase
D: Leucyl-tRNA synthetase
E: Leucyl-tRNA synthetase
F: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)208,1416
Polymers208,1416
Non-polymers00
Water4,143230
1
A: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)34,6901
Polymers34,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)34,6901
Polymers34,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)34,6901
Polymers34,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)34,6901
Polymers34,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)34,6901
Polymers34,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)34,6901
Polymers34,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)232.280, 72.094, 111.249
Angle α, β, γ (deg.)90.00, 95.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Leucyl-tRNA synthetase / LeuRS


Mass: 34690.133 Da / Num. of mol.: 6 / Fragment: UNP residues 252-561 / Mutation: C395S, C533S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Strain: ATCC 50803 / WB clone C6 / Gene: GL50803_8621 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A8BY54, leucine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 2% glycerol, 0.1M Bis-Tris pH 5.8, 2.2M ammonium sulfate, hanging drop, vapor diffusion, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 56769

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.2_432) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WFE

2wfe


Resolution: 2.6→29.849 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 2521 5.01 %
Rwork0.215 --
obs0.2178 50353 88.74 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.252 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9114 Å2-0 Å2-12.0355 Å2
2---10.0871 Å20 Å2
3---7.1757 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11861 0 0 230 12091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712082
X-RAY DIFFRACTIONf_angle_d1.04116480
X-RAY DIFFRACTIONf_dihedral_angle_d14.9414292
X-RAY DIFFRACTIONf_chiral_restr0.0711962
X-RAY DIFFRACTIONf_plane_restr0.0042102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5995-2.69230.35672390.24964625X-RAY DIFFRACTION87
2.6923-2.80010.35372370.25224828X-RAY DIFFRACTION90
2.8001-2.92740.31622730.24834965X-RAY DIFFRACTION93
2.9274-3.08160.30342720.23655102X-RAY DIFFRACTION95
3.0816-3.27440.27192520.22785186X-RAY DIFFRACTION96
3.2744-3.52690.30152530.21825068X-RAY DIFFRACTION95
3.5269-3.88110.2871560.22582998X-RAY DIFFRACTION55
3.8811-4.44120.23152460.18544270X-RAY DIFFRACTION80
4.4412-5.58940.22363180.18215357X-RAY DIFFRACTION99
5.5894-29.85070.25162750.21525433X-RAY DIFFRACTION98

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