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- PDB-2cxa: Crystal structure of Leucyl/phenylalanyl-tRNA protein transferase... -

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Basic information

Entry
Database: PDB / ID: 2cxa
TitleCrystal structure of Leucyl/phenylalanyl-tRNA protein transferase from Escherichia coli
ComponentsLeucyl/phenylalanyl-tRNA-protein transferase
KeywordsTRANSFERASE / aminoacyl-tRNA / protein degradation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
Leucyl/phenylalanyl-tRNA--protein transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKato-Murayama, M. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2007
Title: The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli
Authors: Dong, X. / Kato-Murayama, M. / Muramatsu, T. / Mori, H. / Shirouzu, M. / Bessho, Y. / Yokoyama, S.
History
DepositionJun 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucyl/phenylalanyl-tRNA-protein transferase


Theoretical massNumber of molelcules
Total (without water)29,5481
Polymers29,5481
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.277, 44.784, 76.376
Angle α, β, γ (deg.)90.00, 108.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 29548.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pCA24N / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8P1, lysine/arginine leucyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 1.874262 Å3/Da / Density % sol: 34.374184 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG3350, NaCl, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9797, 0.9795, 0.9680
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2005
RadiationMonochromator: double flat Si(111) crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97951
30.9681
ReflectionResolution: 1.6→36.86 Å / Num. obs: 28862 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.4 Å2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 93.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→36.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1007566.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1408 4.9 %RANDOM
Rwork0.187 ---
obs-28814 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.8448 Å2 / ksol: 0.380198 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-1.73 Å2
2--3.14 Å20 Å2
3----3.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 267 2117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
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_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 250 5.3 %
Rwork0.222 4472 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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