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- PDB-1wfx: Crystal Structure of APE0204 from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 1wfx
TitleCrystal Structure of APE0204 from Aeropyrum pernix
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / RNA 2'-phosphotransferase / tRNA splicing / NAD / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+ ADP-ribosyltransferase activity
Similarity search - Function
ADP-ribosylation fold - #30 / RNA 2'-phosphotransferase, Tpt1/KptA family, N-terminal domain / ADP-ribosylation fold / RNA 2'-phosphotransferase KptA, putative / Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family / Arc Repressor Mutant, subunit A / Alpha-Beta Barrel ...ADP-ribosylation fold - #30 / RNA 2'-phosphotransferase, Tpt1/KptA family, N-terminal domain / ADP-ribosylation fold / RNA 2'-phosphotransferase KptA, putative / Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family / Arc Repressor Mutant, subunit A / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKato-Murayama, M. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of the RNA 2'-Phosphotransferase from Aeropyrum pernix K1
Authors: Kato-Murayama, M. / Bessho, Y. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6417
Polymers21,3981
Non-polymers2436
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable RNA 2'-phosphotransferase
hetero molecules

A: Probable RNA 2'-phosphotransferase
hetero molecules

A: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,92321
Polymers64,1953
Non-polymers72818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5220 Å2
ΔGint-186 kcal/mol
Surface area27020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.667, 102.667, 101.489
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

21A-316-

HOH

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Components

#1: Protein Probable RNA 2'-phosphotransferase / RNA 2'-phosphotransferase / APE0204 protein


Mass: 21398.234 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE0204 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q9YFP5, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.4 Å3/Da / Density % sol: 49 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9789, 0.9791, 0.970
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 6, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97911
30.971
ReflectionResolution: 2.8→44.28 Å / Num. obs: 5217 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 114.6 Å2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→44.07 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1574085.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 536 10.3 %RANDOM
Rwork0.22 ---
obs-5213 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0314 Å2 / ksol: 0.388121 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å23.89 Å20 Å2
2---0.13 Å20 Å2
3---0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 6 16 1464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d22.9
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 75 8.8 %
Rwork0.298 775 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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