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- PDB-5ap8: Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from S. ... -

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Basic information

Entry
Database: PDB / ID: 5ap8
TitleStructure of the SAM-dependent rRNA:acp-transferase Tsr3 from S. solfataricus
ComponentsTSR3
KeywordsTRANSFERASE / S-ADENOSYLMETHIONINE DEPENDENT 3-AMINO-3-CARBOXYPROPYL TRANSFERASE / RRNA / PSEUDOURIDINE / SAM / SPOUT-FOLD
Function / homology
Function and homology information


rRNA small subunit aminocarboxypropyltransferase / rRNA small subunit aminocarboxypropyltransferase activity / enzyme-directed rRNA pseudouridine synthesis / S-adenosyl-L-methionine binding / rRNA binding / cytoplasm
Similarity search - Function
16S/18S rRNA aminocarboxypropyltransferase Tsr3, C-terminal / 16S/18S rRNA aminocarboxypropyltransferase Tsr3 / Ribosome biogenesis protein, C-terminal / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI
Similarity search - Domain/homology
16S rRNA aminocarboxypropyltransferase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.246 Å
AuthorsWurm, J.P. / Immer, C. / Pogoryelov, D. / Meyer, B. / Koetter, P. / Entian, K.-D. / Woehnert, J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Ribosome Biogenesis Factor Tsr3 is the Aminocarboxypropyl Transferase Responsible for 18S Rrna Hypermodification in Yeast and Humans
Authors: Entian, K.-D. / Immer, C. / Koetter, P. / Lafontaine, D. / Britter, M. / Pogoryelov, D. / Sharma, S. / Wohnert, J. / Wurm, J.P.
History
DepositionSep 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TSR3
B: TSR3
C: TSR3


Theoretical massNumber of molelcules
Total (without water)57,6913
Polymers57,6913
Non-polymers00
Water48627
1
A: TSR3


Theoretical massNumber of molelcules
Total (without water)19,2301
Polymers19,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TSR3


Theoretical massNumber of molelcules
Total (without water)19,2301
Polymers19,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TSR3


Theoretical massNumber of molelcules
Total (without water)19,2301
Polymers19,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.590, 62.486, 196.640
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 TSR3


Mass: 19230.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UWV6, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.73 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7.5
Details: 12.5 % MPD, 12.5 % PEG1000, 12.5 % PEG 3350, 100 MM TRIS/BICINE PH 8.5, 30 MM DIETHYLENE GLYCOL,30 MM TRIETHYLENE GLYCOL, 30 MM TETRAETHYLENE GLYCOL, 30 MM PENTAETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.09 Å / Num. obs: 29932 / % possible obs: 99.6 % / Observed criterion σ(I): 1.4 / Redundancy: 3.5 % / Biso Wilson estimate: 64.39 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.39
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 1.41 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.246→48.085 Å / SU ML: 0.33 / σ(F): 1.13 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 2412 4.3 %
Rwork0.2236 --
obs0.2245 29920 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 300 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso mean: 78.1 Å2
Refinement stepCycle: LAST / Resolution: 2.246→48.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 0 27 3741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043768
X-RAY DIFFRACTIONf_angle_d0.7695080
X-RAY DIFFRACTIONf_dihedral_angle_d14.5531413
X-RAY DIFFRACTIONf_chiral_restr0.03604
X-RAY DIFFRACTIONf_plane_restr0.003627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2461-2.2920.43361380.41253004X-RAY DIFFRACTION95
2.292-2.34180.3761400.40283195X-RAY DIFFRACTION100
2.3418-2.39630.36881430.36613125X-RAY DIFFRACTION100
2.3963-2.45620.34031390.33473128X-RAY DIFFRACTION99
2.4562-2.52260.3681400.30733167X-RAY DIFFRACTION100
2.5226-2.59680.30721420.29343199X-RAY DIFFRACTION100
2.5968-2.68070.40121420.283130X-RAY DIFFRACTION100
2.6807-2.77650.25081470.28643167X-RAY DIFFRACTION100
2.7765-2.88760.31371390.25683139X-RAY DIFFRACTION100
2.8876-3.0190.32171390.26653142X-RAY DIFFRACTION99
3.019-3.17810.27381430.27073209X-RAY DIFFRACTION100
3.1781-3.37720.23191450.25253124X-RAY DIFFRACTION100
3.3772-3.63790.24961460.23193179X-RAY DIFFRACTION100
3.6379-4.00380.28271430.2123128X-RAY DIFFRACTION99
4.0038-4.58280.20391360.18123152X-RAY DIFFRACTION100
4.5828-5.77230.19431420.19493166X-RAY DIFFRACTION99
5.7723-48.09550.20531480.18723126X-RAY DIFFRACTION99

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