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- PDB-2z3n: complex structure of LF-transferase and peptide B -

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Basic information

Entry
Database: PDB / ID: 2z3n
Titlecomplex structure of LF-transferase and peptide B
Components
  • Leucyl/phenylalanyl-tRNA-protein transferase
  • peptide (PHE)(ARG)(TYR)(LEU)(GLY)
KeywordsTRANSFERASE / LF-transferase
Function / homology
Function and homology information


lysine/arginine leucyltransferase / leucyl-tRNA--protein transferase activity / aminoacyltransferase activity / protein catabolic process / cytoplasm
Similarity search - Function
Leucyl/phenylalanyl-tRNA-protein transferase, N-terminal domain / Leucyl/phenylalanyl-tRNA-protein transferase, C-terminal domain / Leucyl/phenylalanyl-tRNA-protein transferase / Leucyl/phenylalanyl-tRNA-protein transferase, C-terminal / Leucyl/phenylalanyl-tRNA-protein transferase, N-terminal / Leucyl/phenylalanyl-tRNA protein transferase / Acyl-CoA N-acyltransferase / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich ...Leucyl/phenylalanyl-tRNA-protein transferase, N-terminal domain / Leucyl/phenylalanyl-tRNA-protein transferase, C-terminal domain / Leucyl/phenylalanyl-tRNA-protein transferase / Leucyl/phenylalanyl-tRNA-protein transferase, C-terminal / Leucyl/phenylalanyl-tRNA-protein transferase, N-terminal / Leucyl/phenylalanyl-tRNA protein transferase / Acyl-CoA N-acyltransferase / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Leucyl/phenylalanyl-tRNA--protein transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWatanabe, K. / Toh, Y. / Tomita, K.
CitationJournal: Nature / Year: 2007
Title: Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
Authors: Watanabe, K. / Toh, Y. / Suto, K. / Shimizu, Y. / Oka, N. / Wada, T. / Tomita, K.
History
DepositionJun 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Leucyl/phenylalanyl-tRNA-protein transferase
B: Leucyl/phenylalanyl-tRNA-protein transferase
C: peptide (PHE)(ARG)(TYR)(LEU)(GLY)
D: peptide (PHE)(ARG)(TYR)(LEU)(GLY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6526
Polymers54,3524
Non-polymers3002
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.936, 130.101, 38.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Leucyl/phenylalanyl-tRNA-protein transferase / aminoacyl-tRNA protein transferase / L/F-transferase / Leucyltransferase / Phenyalanyltransferase


Mass: 26520.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Aat / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A8P1, lysine/arginine leucyltransferase
#2: Protein/peptide peptide (PHE)(ARG)(TYR)(LEU)(GLY)


Mass: 655.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM HEPES-Na, 0.7M tri-sodium tartrate, pH 8.0, 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: Apr 8, 2007
RadiationMonochromator: si(111) / Protocol: 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: 20732 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 46.3 Å2 / Rsym value: 0.051 / Net I/σ(I): 41.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1947 / Rsym value: 0.327 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DPS

2dps


Resolution: 2.5→28.74 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1277294.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1042 5.1 %RANDOM
Rwork0.222 ---
obs0.222 20622 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0732 Å2 / ksol: 0.341374 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20 Å2
2--9.25 Å20 Å2
3----11.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 20 10 3800
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 127 5.2 %
Rwork0.303 2330 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramdna-rna.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4dna-rna_rep.paramtar.top
X-RAY DIFFRACTION5tar.paramion.top

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