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- PDB-2yx0: Crystal structure of P. horikoshii TYW1 -

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Basic information

Entry
Database: PDB / ID: 2yx0
TitleCrystal structure of P. horikoshii TYW1
Componentsradical sam enzyme
KeywordsMETAL BINDING PROTEIN / radical sam enzyme / predicted trna modification enzyme / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tRNA 4-demethylwyosine synthase (AdoMet-dependent) / tRNA-4-demethylwyosine synthase activity / tRNA processing / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea / tRNA wybutosine-synthesis / S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase / Wyosine base formation / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea / tRNA wybutosine-synthesis / S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase / Wyosine base formation / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsGoto-Ito, S. / Ishii, R. / Ito, T. / Shibata, R. / Fusatomi, E. / Sekine, S. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis
Authors: Goto-Ito, S. / Ishii, R. / Ito, T. / Shibata, R. / Fusatomi, E. / Sekine, S. / Bessho, Y. / Yokoyama, S.
History
DepositionApr 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: radical sam enzyme


Theoretical massNumber of molelcules
Total (without water)39,8991
Polymers39,8991
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.920, 60.850, 153.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein radical sam enzyme / Hypothetical protein PH1705


Mass: 39899.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pet11b / Production host: Escherichia coli (E. coli) / References: UniProt: O59412
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A10.97898
SYNCHROTRONPhoton Factory BL-5A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 3, 2006
ADSC QUANTUM 3152CCDJun 15, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
211
ReflectionResolution: 2.2→500 Å / Num. obs: 20441 / Biso Wilson estimate: 18.9 Å2

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.21→31.49 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1608210.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 923 5.1 %RANDOM
Rwork0.194 ---
obs0.194 18175 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9115 Å2 / ksol: 0.323486 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.3 Å20 Å20 Å2
2--0.52 Å20 Å2
3----6.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.21→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 0 113 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.061.5
X-RAY DIFFRACTIONc_mcangle_it6.192
X-RAY DIFFRACTIONc_scbond_it8.252
X-RAY DIFFRACTIONc_scangle_it9.52.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 94 5.6 %
Rwork0.244 1582 -
obs--49.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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