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- PDB-2olw: Crystal Structure of E. coli pseudouridine synthase RluE -

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Basic information

Entry
Database: PDB / ID: 2olw
TitleCrystal Structure of E. coli pseudouridine synthase RluE
ComponentsRibosomal large subunit pseudouridine synthase E
KeywordsISOMERASE / bifurcated beta sheet
Function / homology
Function and homology information


23S rRNA pseudouridine2457 synthase / 23S rRNA pseudouridine(2457) 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 / enzyme-directed rRNA 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, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / 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, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, catalytic domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Ribosomal large subunit pseudouridine synthase E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPan, H. / Ho, J.D. / Stroud, R.M. / Finer-Moore, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of E. coli rRNA Pseudouridine Synthase RluE.
Authors: Pan, H. / Ho, J.D. / Stroud, R.M. / Finer-Moore, J.
History
DepositionJan 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal large subunit pseudouridine synthase E
B: Ribosomal large subunit pseudouridine synthase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,44110
Polymers49,8312
Non-polymers6118
Water4,630257
1
A: Ribosomal large subunit pseudouridine synthase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1324
Polymers24,9151
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal large subunit pseudouridine synthase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3106
Polymers24,9151
Non-polymers3945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.015, 78.887, 84.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological form of the protein is a monomer

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Components

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


Mass: 24915.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rluE / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P75966, Isomerases; Intramolecular transferases; Transferring other groups
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 1.97 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4 mg/ml protein in 10 mM Tris, pH 7.5, with 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate and 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, ...Details: 4 mg/ml protein in 10 mM Tris, pH 7.5, with 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate and 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 12, 2003 / Details: double crystal monochrometer
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 49168 / % possible obs: 93.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.096 / Χ2: 1.286 / Net I/σ(I): 14
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5102 / Χ2: 1.127 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ELVESrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KSV with the N-terminal domain removed

1ksv


Resolution: 1.6→28.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 1.692 / SU ML: 0.062 / Isotropic thermal model: isotropic with restraints / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2319 5.1 %RANDOM
Rwork0.213 ---
all0.215 45764 --
obs0.215 45764 86.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.928 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.03 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.6→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 13 281 3129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222927
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9853982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58522.836134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87415470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0791532
X-RAY DIFFRACTIONr_chiral_restr0.0950.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022264
X-RAY DIFFRACTIONr_nbd_refined0.1980.21235
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.222
X-RAY DIFFRACTIONr_mcbond_it1.1951.51843
X-RAY DIFFRACTIONr_mcangle_it1.95422904
X-RAY DIFFRACTIONr_scbond_it2.83131228
X-RAY DIFFRACTIONr_scangle_it4.2454.51078
LS refinement shellResolution: 1.6→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 218 -
Rwork0.211 3531 -
obs-3749 97.35 %

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