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- PDB-3pz5: The crystal structure of AaLeuRS-CP1-D20 -

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Basic information

Entry
Database: PDB / ID: 3pz5
TitleThe crystal structure of AaLeuRS-CP1-D20
ComponentsLeucyl-tRNA synthetase subunit alpha
KeywordsLIGASE / Editing domain
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytosol
Similarity search - Function
Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / 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 subunit alpha
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, R.J. / 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_ncs_dom_lim / struct_ref_seq_dif
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_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucyl-tRNA synthetase subunit alpha
B: Leucyl-tRNA synthetase subunit alpha


Theoretical massNumber of molelcules
Total (without water)45,3652
Polymers45,3652
Non-polymers00
Water1,27971
1
A: Leucyl-tRNA synthetase subunit alpha


Theoretical massNumber of molelcules
Total (without water)22,6831
Polymers22,6831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucyl-tRNA synthetase subunit alpha


Theoretical massNumber of molelcules
Total (without water)22,6831
Polymers22,6831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.143, 106.143, 81.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 229 - 417 / Label seq-ID: 11 - 179

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

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Components

#1: Protein Leucyl-tRNA synthetase subunit alpha / Leucine--tRNA ligase subunit alpha / LeuRS


Mass: 22682.658 Da / Num. of mol.: 2 / Fragment: UNP residues 228-439 / Mutation: P241L, Deletion of residues 242-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: leuS, aq_351 / Plasmid: PET30b / Production host: Escherichia coli (E. coli) / References: UniProt: O66680, leucine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30 % PEG 4000, 0.1 M sodium citrate tribasic dihydrate at pH 5.6 and 0.2 M ammonium acetate , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15748
Reflection shellResolution: 2.5→2.59 Å / % possible all: 79.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 2.5→37.53 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.133 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 739 4.9 %RANDOM
Rwork0.2126 ---
obs0.2151 14949 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.82 Å2 / Biso mean: 33.2859 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---1.75 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 0 71 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223083
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9594181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9925381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60524.366142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93315510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5441516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212362
X-RAY DIFFRACTIONr_mcbond_it0.3991.51897
X-RAY DIFFRACTIONr_mcangle_it0.74923050
X-RAY DIFFRACTIONr_scbond_it0.79631186
X-RAY DIFFRACTIONr_scangle_it1.4234.51131
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1468 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.260.5
MEDIUM THERMAL0.122
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 48 -
Rwork0.256 842 -
all-890 -
obs--77.73 %

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