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- PDB-2cxi: Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-t... -

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Basic information

Entry
Database: PDB / ID: 2cxi
TitleCrystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii
ComponentsPhenylalanyl-tRNA synthetase beta chain
KeywordsLIGASE / 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


phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / magnesium ion binding / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanine-tRNA ligase beta chain 2, archaeal type / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain ...Phenylalanine-tRNA ligase beta chain 2, archaeal type / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Putative DNA-binding domain superfamily / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phenylalanine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsSasaki, H. / Sekine, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase
Authors: Sasaki, H.M. / Sekine, S. / Sengoku, T. / Fukunaga, R. / Hattori, M. / Utsunomiya, Y. / Kuroishi, C. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase beta chain
B: Phenylalanyl-tRNA synthetase beta chain
C: Phenylalanyl-tRNA synthetase beta chain


Theoretical massNumber of molelcules
Total (without water)122,7473
Polymers122,7473
Non-polymers00
Water12,322684
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.779, 81.973, 139.096
Angle α, β, γ (deg.)90.00, 116.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phenylalanyl-tRNA synthetase beta chain / Phenylalanine--tRNA ligase beta chain / PheRS / PheRS beta


Mass: 40915.605 Da / Num. of mol.: 3 / Fragment: N-terminal fragment(residues 1-348)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0657 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: O73984, phenylalanine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 293 K / Method: microbatch, modified / pH: 5.6
Details: PEG 20000, sodium citrate, pH 5.6, Microbatch, modified, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97928, 0.97960, 0.98400
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2005
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979281
20.97961
30.9841
ReflectionResolution: 1.94→50 Å / Num. obs: 104810 / % possible obs: 99.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.94→2.01 Å / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.94→41.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.264 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 5267 5 %RANDOM
Rwork0.18766 ---
obs0.18981 99536 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.245 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 0 684 9210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.97611706
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47151029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34624.307411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.731151710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0821560
X-RAY DIFFRACTIONr_chiral_restr0.120.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.24035
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2710
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.311.55392
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73528382
X-RAY DIFFRACTIONr_scbond_it3.09133859
X-RAY DIFFRACTIONr_scangle_it4.6784.53324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.942→1.993 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 369
Rwork0.252 6637

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