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- PDB-2e21: Crystal structure of TilS in a complex with AMPPNP from Aquifex a... -

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Basic information

Entry
Database: PDB / ID: 2.0E+21
TitleCrystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.
ComponentstRNA(Ile)-lysidine synthase
KeywordsLIGASE / Rossmann-fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tRNAIle-lysidine synthase / ligase activity, forming carbon-nitrogen bonds / tRNA modification / ATP binding / cytoplasm
Similarity search - Function
: / TilS-like substrate binding domain / Chorismate Mutase Domain, subunit A - #20 / tRNA(Ile)-lysidine synthase / tRNA(Ile)-lysidine synthase, N-terminal / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Chorismate Mutase Domain, subunit A / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...: / TilS-like substrate binding domain / Chorismate Mutase Domain, subunit A - #20 / tRNA(Ile)-lysidine synthase / tRNA(Ile)-lysidine synthase, N-terminal / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Chorismate Mutase Domain, subunit A / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / tRNA(Ile)-lysidine synthase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKuratani, M. / Yoshikawa, Y. / Sekine, S. / Ishii, T. / Shibata, R. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine
Authors: Kuratani, M. / Yoshikawa, Y. / Bessho, Y. / Higashijima, K. / Ishii, T. / Shibata, R. / Takahashi, S. / Yutani, K. / Yokoyama, S.
History
DepositionNov 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: tRNA(Ile)-lysidine synthase
B: tRNA(Ile)-lysidine synthase
C: tRNA(Ile)-lysidine synthase
D: tRNA(Ile)-lysidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,5716
Polymers149,5584
Non-polymers1,0122
Water3,243180
1
A: tRNA(Ile)-lysidine synthase
B: tRNA(Ile)-lysidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2853
Polymers74,7792
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-36 kcal/mol
Surface area29770 Å2
MethodPISA, PQS
2
C: tRNA(Ile)-lysidine synthase
D: tRNA(Ile)-lysidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2853
Polymers74,7792
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-34 kcal/mol
Surface area29730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.456, 82.231, 109.431
Angle α, β, γ (deg.)90.00, 105.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tRNA(Ile)-lysidine synthase / tRNA(Ile)-lysidine synthetase / tRNA(Ile)-2-lysyl-cytidine synthase


Mass: 37389.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: tilS / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O67728, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M Na citrate, 0.2M Ammonium Acetate, 20% PEG 4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 46600 / Num. obs: 46266 / % possible obs: 0.992 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.088 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.442 / % possible all: 93

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WY5

1wy5


Resolution: 2.7→49.01 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1537074.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2199 5 %RANDOM
Rwork0.222 ---
all0.226 46226 --
obs0.222 44291 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.8621 Å2 / ksol: 0.32042 e/Å3
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1--11.2 Å20 Å210.6 Å2
2--1.24 Å20 Å2
3---9.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10448 0 62 180 10690
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 326 4.6 %
Rwork0.337 6777 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4AMPPNP.param

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