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- PDB-2z3k: complex structure of LF-transferase and rAF -

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Basic information

Entry
Database: PDB / ID: 2z3k
Titlecomplex structure of LF-transferase and rAF
ComponentsLeucyl/phenylalanyl-tRNA-protein transferase
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
PHENYLALANINE / D(-)-TARTARIC ACID / Chem-XYA / Leucyl/phenylalanyl-tRNA--protein transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 ...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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2068
Polymers53,0412
Non-polymers1,1656
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.106, 129.846, 38.691
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: Chemical ChemComp-XYA / 2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 9-BETA-D-XYLOFURANOSYL-ADENINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: 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: 2.72 Å3/Da / Density % sol: 54.85 %
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: Feb 16, 2007
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14014 / % possible obs: 98.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 57.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 26.4
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1202 / Rsym value: 0.313 / % possible all: 84.1

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Processing

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

2dps


Resolution: 2.85→28.85 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 198399.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 659 4.9 %RANDOM
Rwork0.202 ---
obs0.202 13386 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.839 Å2 / ksol: 0.316563 e/Å3
Displacement parametersBiso mean: 58.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.12 Å20 Å20 Å2
2--4.52 Å20 Å2
3----18.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.85→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 60 30 3784
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.611.5
X-RAY DIFFRACTIONc_mcangle_it7.482
X-RAY DIFFRACTIONc_scbond_it6.022
X-RAY DIFFRACTIONc_scangle_it9.142.5
LS refinement shellResolution: 2.85→2.98 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 61 4.7 %
Rwork0.309 1230 -
obs--72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_dna3pendo_Aat.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4tar.paramtar.top

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