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- PDB-3o0a: Crystal structure of the wild type CP1 hydrolitic domain from Aqu... -

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Basic information

Entry
Database: PDB / ID: 3o0a
TitleCrystal structure of the wild type CP1 hydrolitic domain from Aquifex Aeolicus leucyl-trna
ComponentsLeucyl-tRNA synthetase subunit alpha
KeywordsLIGASE / AQUIFEX AEOLICUS / LEUCYL-TRNA SYNTHETASE / CP1 HYDROLYTIC DOMAIN / AMINOACYL-TRNA SYNTHETASE / ATP-BINDING / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS
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: 1.77 Å
AuthorsCura, V. / Olieric, N. / Wang, E.-D. / Moras, D. / Eriani, G. / Cavarelli, J.
Citation
Journal: To be Published
Title: Crystal Structure of the Wild Type and Two Mutants of the Cp1 Hydrolytic Domain from Aquifex Aeolicus Leucyl-tRNA Synthetase
Authors: Cura, V. / Olieric, N. / Guichard, A. / Wang, E.-D. / Moras, D. / Eriani, G. / Cavarelli, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and Preliminary X-Ray Crystallographic Study of the Wild Type and Two Mutants of the Cp1 Hydrolytic Domain from Aquifex Aeolicus Leucyl-tRNA Synthetase
Authors: Cura, V. / Olieric, N. / Guichard, A. / Wang, E.-D. / Moras, D. / Eriani, G. / Cavarelli, J.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)49,7892
Polymers49,7892
Non-polymers00
Water9,242513
1
A: Leucyl-tRNA synthetase subunit alpha


Theoretical massNumber of molelcules
Total (without water)24,8941
Polymers24,8941
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)24,8941
Polymers24,8941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.689, 98.180, 116.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24894.338 Da / Num. of mol.: 2 / Fragment: HYDROLYTIC DOMAIN (UNP RESIDUES 225-443)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: leuS, aq_351 / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O66680, leucine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growpH: 8.5
Details: 2.1 M AMMONIUM SULFATE, 100 MM TRIS -HCL PH 8.5, 10 MM POTASSIUM CHLORIDE, 1 MM CALCIUM CHLORIDE, 1% PEG 400 FOR 30S, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K, PH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.77→36.15 Å / Num. obs: 43042 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.03
Reflection shellResolution: 1.77→1.82 Å / Rmerge(I) obs: 0.084 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 1.77→36.15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.525 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3284 7.6 %RANDOM
Rwork0.188 ---
obs0.191 43042 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.197 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.87 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.77→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 0 513 3910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223480
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9724710
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62624.663163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85415613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8181518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21734
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22399
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2426
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6881.52163
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14623415
X-RAY DIFFRACTIONr_scbond_it1.89531504
X-RAY DIFFRACTIONr_scangle_it3.044.51295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 242 -
Rwork0.191 2920 -
obs--98.47 %
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)
10.71080.09310.16620.77240.54262.271-0.0260.03370.071-0.1355-0.12650.0778-0.1711-0.18750.1525-0.05660.0195-0.022-0.0591-0.0349-0.041519.148993.593358.6075
20.5403-0.0819-0.10762.0719-0.72270.8836-0.01010.0784-0.0044-0.25750.03340.08180.136-0.0432-0.0232-0.0488-0.0234-0.0095-0.0350.0308-0.042918.552173.531426.153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A228 - 438
2X-RAY DIFFRACTION2B228 - 441

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