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- PDB-1qyu: Structure of the catalytic domain of 23S rRNA pseudouridine synth... -

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Basic information

Entry
Database: PDB / ID: 1qyu
TitleStructure of the catalytic domain of 23S rRNA pseudouridine synthase RluD
ComponentsRibosomal large subunit pseudouridine synthase D
KeywordsLYASE / CATALYTIC DOMAIN / RLUD / PSEUDOURIDINE SYNTHASE
Function / homology
Function and homology information


23S rRNA pseudouridine1911/1915/1917 synthase / 23S rRNA pseudouridine(1911/1915/1917) synthase activity / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol
Similarity search - Function
Helix Hairpins - #230 / Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / Helix Hairpins ...Helix Hairpins - #230 / Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / Helix Hairpins / Helix non-globular / Special / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal large subunit pseudouridine synthase D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsDel Campo, M. / Ofengand, J. / Malhotra, A.
CitationJournal: RNA / Year: 2004
Title: Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli
Authors: Del Campo, M. / Ofengand, J. / Malhotra, A.
History
DepositionSep 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 D


Theoretical massNumber of molelcules
Total (without water)40,2511
Polymers40,2511
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.140, 75.140, 181.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein Ribosomal large subunit pseudouridine synthase D / E.C.4.2.1.70 / E. coli 23S RNA pseudouridine synthase RluD / Pseudouridylate synthase / Uracil hydrolyase / ftsH ...E. coli 23S RNA pseudouridine synthase RluD / Pseudouridylate synthase / Uracil hydrolyase / ftsH suppressor protein SfhB


Mass: 40250.992 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RLUD / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33643, pseudouridylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 4.04 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Del Campo, M., (2003) Acta Cryst., D59, 1871.
Components of the solutions
*PLUS
Conc.: 25-40 % / Common name: ethylene glycol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.978795, 0.978462, 0.950037
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 7, 2002
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9787951
20.9784621
30.9500371
ReflectionResolution: 2→50 Å / Num. all: 34611 / Num. obs: 36112 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 38.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 9.2 / % possible all: 69.6
Reflection
*PLUS
Highest resolution: 2 Å
Reflection shell
*PLUS
% possible obs: 69.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→39.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2431360.77 / 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
Rfree0.232 1573 4.9 %RANDOM
Rwork0.219 ---
all-36112 --
obs-32009 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7351 Å2 / ksol: 0.334718 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.82 Å20 Å20 Å2
2--6.82 Å20 Å2
3----13.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 0 261 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.772
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 191 5.2 %
Rwork0.248 3507 -
obs--62.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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