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- PDB-3a5z: Crystal structure of Escherichia coli GenX in complex with elonga... -

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Basic information

Entry
Database: PDB / ID: 3a5z
TitleCrystal structure of Escherichia coli GenX in complex with elongation factor P
Components
  • Elongation factor P
  • Putative lysyl-tRNA synthetase
KeywordsLIGASE / aminoacyl-tRNA synthetase paralog / Translation / tRNA / Lysyl-tRNA synthetase / Elongation Factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Aminoacyl-tRNA synthetase
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 / negative regulation of translational frameshifting / translational elongation / translation elongation factor activity / rescue of stalled ribosome ...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 / negative regulation of translational frameshifting / translational elongation / translation elongation factor activity / rescue of stalled ribosome / ribosome binding / tRNA binding / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Elongation factor P--(R)-beta-lysine ligase / Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor P / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal ...Elongation factor P--(R)-beta-lysine ligase / Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor P / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal / Elongation factor P (EF-P) OB domain / Translation elongation factor, KOW-like / Elongation factor P (EF-P) KOW-like domain / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / SH3 type barrels. - #30 / 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) / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Elongation factor P--(R)-beta-lysine ligase / Elongation factor P / Elongation factor P / Elongation factor P--(R)-beta-lysine ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: Putative lysyl-tRNA synthetase
B: Elongation factor P
C: Putative lysyl-tRNA synthetase
D: Elongation factor P
E: Putative lysyl-tRNA synthetase
F: Elongation factor P
G: Putative lysyl-tRNA synthetase
H: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,67312
Polymers232,7758
Non-polymers1,8984
Water4,125229
1
A: Putative lysyl-tRNA synthetase
B: Elongation factor P
C: Putative lysyl-tRNA synthetase
D: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3376
Polymers116,3884
Non-polymers9492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-32 kcal/mol
Surface area40270 Å2
MethodPISA
2
E: Putative lysyl-tRNA synthetase
F: Elongation factor P
G: Putative lysyl-tRNA synthetase
H: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3376
Polymers116,3884
Non-polymers9492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-28 kcal/mol
Surface area36130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.930, 102.960, 119.940
Angle α, β, γ (deg.)90.00, 99.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative lysyl-tRNA synthetase / GenX


Mass: 37299.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC4100 / Gene: genX, ECs5136 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3SGA2, UniProt: P0A8N7*PLUS, lysine-tRNA ligase
#2: Protein
Elongation factor P / / EF-P


Mass: 20894.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: efp, ECs5128 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3SGD7, UniProt: P0A6N4*PLUS
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Na/Cacodylate, Ammonium Sulfate, PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 82592 / % possible obs: 93.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 39 Å2 / Rsym value: 0.058
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.357 / % possible all: 67.4

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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: 3A5Y, 1UEB

3a5y

1ueb


Resolution: 2.5→45.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 904336.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4162 5 %RANDOM
Rwork0.226 ---
obs0.226 82571 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0015 Å2 / ksol: 0.323962 e/Å3
Displacement parametersBiso mean: 63.3 Å2
Baniso -1Baniso -2Baniso -3
1-6 Å20 Å2-20.58 Å2
2---9.33 Å20 Å2
3---3.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14608 0 128 229 14965
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 490 4.7 %
Rwork0.367 9979 -
obs--71.7 %
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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