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- PDB-1ksv: STRUCTURE OF RSUA -

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Basic information

Entry
Database: PDB / ID: 1ksv
TitleSTRUCTURE OF RSUA
ComponentsRIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A
KeywordsLYASE / Pseudouridine Synthase / rsuA
Function / homology
Function and homology information


16S rRNA pseudouridine516 synthase / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol
Similarity search - Function
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 TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily ...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 TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Ribosomal small subunit pseudouridine synthase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSivaraman, J. / Sauve, V. / Larocque, R. / Stura, E.A. / Schrag, J.D. / Cygler, M. / Matte, A.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP.
Authors: Sivaraman, J. / Sauve, V. / Larocque, R. / Stura, E.A. / Schrag, J.D. / Cygler, M. / Matte, A.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6952
Polymers26,3711
Non-polymers3241
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.061, 147.580, 34.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A / / 16S PSEUDOURIDYLATE 516 SYNTHASE / 16S PSEUDOURIDINE 516 SYNTHASE / URACIL HYDROLYASE


Mass: 26371.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P0AA43, pseudouridylate synthase
#2: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG3350, Malate, KSCN, Isoproponal, Glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 18K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 24, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→45 Å / Num. all: 12874 / Num. obs: 12874 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.064 / Net I/σ(I): 16
Reflection shellResolution: 2.65→2.74 Å / Rsym value: 0.257 / % possible all: 76.6

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→45 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 906 RANDOM
Rwork0.21 --
all-12862 -
obs-12862 -
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.65→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 21 180 2029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.88

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