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- PDB-3pz0: The crystal structure of AaLeuRS-CP1 -

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Basic information

Entry
Database: PDB / ID: 3pz0
TitleThe crystal structure of AaLeuRS-CP1
ComponentsLeucyl-tRNA synthetase subunit alpha
KeywordsLIGASE / Editing domain / AaLeuRS_CP1
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm
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: 2.4 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 13, 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 ...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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: Leucyl-tRNA synthetase subunit alpha
B: Leucyl-tRNA synthetase subunit alpha
C: Leucyl-tRNA synthetase subunit alpha
D: Leucyl-tRNA synthetase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4425
Polymers100,4024
Non-polymers401
Water1,72996
1
A: Leucyl-tRNA synthetase subunit alpha


Theoretical massNumber of molelcules
Total (without water)25,1011
Polymers25,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucyl-tRNA synthetase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1412
Polymers25,1011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leucyl-tRNA synthetase subunit alpha


Theoretical massNumber of molelcules
Total (without water)25,1011
Polymers25,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leucyl-tRNA synthetase subunit alpha


Theoretical massNumber of molelcules
Total (without water)25,1011
Polymers25,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.958, 94.565, 118.309
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A228 - 439
2114B228 - 439
3114C228 - 439

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Components

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


Mass: 25100.500 Da / Num. of mol.: 4 / Fragment: UNP residues 228-439
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 17 % polyethylene glycol 8000 (PEG 8000), 0.1 M sodium cacodylate trihydrate pH 6.8 and 0.2 M calcium acetate hydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33791
Reflection shellResolution: 2.4→2.46 Å / % possible all: 80.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PZ5

3pz5


Resolution: 2.4→34.51 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.725 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27369 1520 5 %RANDOM
Rwork0.21692 ---
obs0.21978 28699 89.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.444 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20.16 Å2
2---0.4 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 1 96 6757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9679247
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44224.54315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.477151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9471536
X-RAY DIFFRACTIONr_chiral_restr0.0760.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215208
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4381.54192
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54626751
X-RAY DIFFRACTIONr_scbond_it3.95132628
X-RAY DIFFRACTIONr_scangle_it6.224.52496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1648 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.250.5
Bmedium positional0.330.5
Cmedium positional0.290.5
Amedium thermal0.532
Bmedium thermal0.552
Cmedium thermal0.52
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 100 -
Rwork0.264 1874 -
obs--80.05 %

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