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- PDB-1yy3: Structure of S-Adenosylmethionine:tRNA Ribosyltransferase-Isomera... -

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Basic information

Entry
Database: PDB / ID: 1yy3
TitleStructure of S-Adenosylmethionine:tRNA Ribosyltransferase-Isomerase (QueA)
ComponentsS-adenosylmethionine:tRNA ribosyltransferase-isomerase
KeywordsISOMERASE / beta-barrel / QueA / Bacillus subtilis / Quein Queuosine / S-Adenosylmethionine:tRNA Ribosyltransferase-Isomerase / tRNA-modification
Function / homology
Function and homology information


S-adenosylmethionine:tRNA ribosyltransferase-isomerase / S-adenosylmethionine:tRNA ribosyltransferase-isomerase activity / tRNA wobble guanine modification / queuosine biosynthetic process / cytoplasm
Similarity search - Function
QueA-like / QueA-like / QueA-like / S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA / S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA superfamily / QueA, domain 1 / QueA, domain 2 / Queuosine biosynthesis protein / Thrombin, subunit H / Beta Barrel ...QueA-like / QueA-like / QueA-like / S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA / S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA superfamily / QueA, domain 1 / QueA, domain 2 / Queuosine biosynthesis protein / Thrombin, subunit H / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine:tRNA ribosyltransferase-isomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.88 Å
AuthorsGrimm, C. / Ficner, R. / Reuter, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase
Authors: Grimm, C. / Ficner, R. / Sgraja, T. / Haebel, P. / Klebe, G. / Reuter, K.
History
DepositionFeb 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine:tRNA ribosyltransferase-isomerase
B: S-adenosylmethionine:tRNA ribosyltransferase-isomerase


Theoretical massNumber of molelcules
Total (without water)77,6802
Polymers77,6802
Non-polymers00
Water00
1
A: S-adenosylmethionine:tRNA ribosyltransferase-isomerase


Theoretical massNumber of molelcules
Total (without water)38,8401
Polymers38,8401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-adenosylmethionine:tRNA ribosyltransferase-isomerase


Theoretical massNumber of molelcules
Total (without water)38,8401
Polymers38,8401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.671, 101.671, 152.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsEach of the two chains represents a biological unit

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Components

#1: Protein S-adenosylmethionine:tRNA ribosyltransferase-isomerase / Queuosine biosynthesis protein queA


Mass: 38840.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O32054, Isomerases

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9393
SYNCHROTRONESRF ID2920.9787, 0.9789, 0.9205
SYNCHROTRONESRF ID14-430.9999, 1.009, 0.9393, 0.9919
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 1, 2000
MARRESEARCH2CCD
ADSC QUANTUM 43CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
3MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97871
30.97891
40.92051
50.99991
61.0091
70.99191
ReflectionResolution: 2.7→61 Å / Num. obs: 41787 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Biso Wilson estimate: 95.6 Å2 / Rsym value: 0.053 / Net I/σ(I): 27.9
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.33 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.88→61 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1811543.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.386 734 4 %RANDOM
Rwork0.364 ---
obs0.364 18507 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1349 Å2 / ksol: 0.342883 e/Å3
Displacement parametersBiso mean: 86.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.27 Å20 Å20 Å2
2---7.27 Å20 Å2
3---14.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.81 Å
Luzzati d res low-5 Å
Luzzati sigma a1.12 Å0.86 Å
Refinement stepCycle: LAST / Resolution: 2.88→61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4990 0 0 0 4990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
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
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.88→3.04 Å / Rfactor Rfree: 0.5996 / Rfactor Rwork: 0.5921 / Total num. of bins used: 5
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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