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- PDB-3a5y: Crystal structure of GenX from Escherichia coli in complex with l... -

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Basic information

Entry
Database: PDB / ID: 3a5y
TitleCrystal structure of GenX from Escherichia coli in complex with lysyladenylate analog
ComponentsPutative lysyl-tRNA synthetase
KeywordsLIGASE / Aminoacyl-tRNA synthetase paralog / Translation / tRNA / Lysyl-tRNA synthetase / Lysyladenylate analog / Aminoacyl-tRNA synthetase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein-lysine lysyltransferase activity / acid-ammonia (or amide) ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-ammonia (or amine) ligases (amide synthases) / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / cellular response to acidic pH / tRNA binding / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Elongation factor P--(R)-beta-lysine ligase / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Elongation factor P--(R)-beta-lysine ligase / Elongation factor P--(R)-beta-lysine ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSumida, T. / Yanagisawa, T. / Ishii, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
Authors: Yanagisawa, T. / Sumida, T. / Ishii, R. / Takemoto, C. / Yokoyama, S.
History
DepositionAug 17, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 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 / 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 / _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

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Assembly

Deposited unit
A: Putative lysyl-tRNA synthetase
B: Putative lysyl-tRNA synthetase
C: Putative lysyl-tRNA synthetase
D: Putative lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,6518
Polymers156,7534
Non-polymers1,8984
Water18,5731031
1
A: Putative lysyl-tRNA synthetase
B: Putative lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3264
Polymers78,3772
Non-polymers9492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-17 kcal/mol
Surface area24170 Å2
MethodPISA
2
C: Putative lysyl-tRNA synthetase
D: Putative lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3264
Polymers78,3772
Non-polymers9492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-20 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.800, 69.150, 94.080
Angle α, β, γ (deg.)95.47, 106.51, 90.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative lysyl-tRNA synthetase / GenX


Mass: 39188.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC4100 / Gene: ECs5136, GenX / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3SGA2, UniProt: P0A8N7*PLUS, lysine-tRNA ligase
#2: Chemical
ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N8O7S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1031 / 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: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Hepes-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 99019 / % possible obs: 95.4 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.086
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.278 / % possible all: 77.9

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Processing

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

1lyl


Resolution: 1.9→44.87 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 785972.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 9925 10 %RANDOM
Rwork0.171 ---
obs0.171 99017 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.9354 Å2 / ksol: 0.365538 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.75 Å2-3.62 Å20.19 Å2
2--6.73 Å2-4.37 Å2
3----2.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9876 0 128 1031 11035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it3.861.5
X-RAY DIFFRACTIONc_mcangle_it4.592
X-RAY DIFFRACTIONc_scbond_it5.982
X-RAY DIFFRACTIONc_scangle_it7.62.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 1473 10.3 %
Rwork0.226 12791 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4refmacAMS.paramrefmacAMS.top

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