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- PDB-2gml: Crystal Structure of Catalytic Domain of E.coli RluF -

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Basic information

Entry
Database: PDB / ID: 2gml
TitleCrystal Structure of Catalytic Domain of E.coli RluF
ComponentsRibosomal large subunit pseudouridine synthase F
KeywordsISOMERASE / pseudouridine synthase / RluF / ribosome / RNA modifying enzyme
Function / homology
Function and homology information


23S rRNA pseudouridine2604 synthase / 23S rRNA pseudouridine(2604) synthase activity / maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) / maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) / rRNA pseudouridine synthase activity / Isomerases; Intramolecular transferases; Transferring other groups / tRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / tRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding
Similarity search - Function
Alpha-L RNA-binding motif / Pseudouridine synthase, RsuA/RluB/E/F, catalytic domain / Pseudouridine synthase, RsuA/RluB/E/F / Pseudouridine synthase, RsuA/RluB/E/F, conserved site / Rsu family of pseudouridine synthase signature. / Pseudouridine synthase I, catalytic domain, N-terminal subdomain / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase, catalytic domain superfamily ...Alpha-L RNA-binding motif / Pseudouridine synthase, RsuA/RluB/E/F, catalytic domain / Pseudouridine synthase, RsuA/RluB/E/F / Pseudouridine synthase, RsuA/RluB/E/F, conserved site / Rsu family of pseudouridine synthase signature. / Pseudouridine synthase I, catalytic domain, N-terminal subdomain / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase, catalytic domain superfamily / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dual-specificity RNA pseudouridine synthase RluF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsSunita, S. / Zhenxing, H. / Swaathi, J. / Cygler, M. / Matte, A. / Sivaraman, J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Domain Organization and Crystal Structure of the Catalytic Domain of E.coli RluF, a Pseudouridine Synthase that Acts on 23S rRNA
Authors: Sunita, S. / Zhenxing, H. / Swaathi, J. / Cygler, M. / Matte, A. / Sivaraman, J.
History
DepositionApr 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal large subunit pseudouridine synthase F
B: Ribosomal large subunit pseudouridine synthase F


Theoretical massNumber of molelcules
Total (without water)53,6352
Polymers53,6352
Non-polymers00
Water2,252125
1
A: Ribosomal large subunit pseudouridine synthase F


Theoretical massNumber of molelcules
Total (without water)26,8181
Polymers26,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal large subunit pseudouridine synthase F


Theoretical massNumber of molelcules
Total (without water)26,8181
Polymers26,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.714, 65.714, 215.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ribosomal large subunit pseudouridine synthase F / rRNA-uridine isomerase F / rRNA pseudouridylate synthase F


Mass: 26817.506 Da / Num. of mol.: 2 / Fragment: residues (-11)-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pF04 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P32684, Isomerases; Intramolecular transferases; Transferring other groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 0.2M potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792, 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
ReflectionResolution: 2.6→50 Å / Num. obs: 27726 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.8

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Processing

Software
NameClassification
ADSCdata collection
DENZOdata reduction
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→45 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.287 2140 RANDOM
Rwork0.225 --
obs-27555 -
Refinement stepCycle: LAST / Resolution: 2.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 0 125 2750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6

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