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- PDB-2oml: crystal structure of E. coli pseudouridine synthase RluE -

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Basic information

Entry
Database: PDB / ID: 2oml
Titlecrystal structure of E. coli pseudouridine synthase RluE
ComponentsRibosomal large subunit pseudouridine synthase E
KeywordsISOMERASE / bifurcated beta sheet / thrombin-cleaved
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 / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / 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, RsuA/RluA-like / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / RNA pseudouridylate synthase / Pseudouridine synthase, catalytic domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal large subunit pseudouridine synthase E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0177
Polymers21,4401
Non-polymers5766
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.310, 56.780, 91.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biologically active 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: 21440.342 Da / Num. of mol.: 1 / Fragment: catalytic domain
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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4 mg/ml protein in 10 mM Tris, pH 7.5, 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate, crystals were improved by ...Details: 4 mg/ml protein in 10 mM Tris, pH 7.5, 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate, crystals were improved by microseeding a solution of 18-22% MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate and 2 mg/ml protein at 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: 0.954
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2003 / Details: double crystal monochrometer
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 13.7 / Number: 241836 / Rmerge(I) obs: 0.063 / Χ2: 1.12 / D res high: 1.2 Å / D res low: 40 Å / Num. obs: 52181 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
2.594099.310.0340.817
2.052.5999.810.0540.901
1.792.0599.710.0731.09
1.631.799910.1071.136
1.511.6398.710.1571.288
1.421.5198.310.2471.171
1.351.4297.910.3661.205
1.291.3597.310.5141.208
1.241.2996.610.6731.279
1.21.249410.7131.277
ReflectionResolution: 1.2→40 Å / Num. obs: 52181 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.125 / Net I/σ(I): 13.7
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4929 / Χ2: 1.277 / % possible all: 94

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Processing

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

1ksv


Resolution: 1.2→28.08 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.2 / SU ML: 0.024
Isotropic thermal model: restrained individual anisotropic B-factor refinement
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 4982 10 %RANDOM
Rwork0.149 ---
all0.152 49576 --
obs0.152 49576 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.2→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 30 191 1664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221495
X-RAY DIFFRACTIONr_bond_other_d0.0020.021029
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9912039
X-RAY DIFFRACTIONr_angle_other_deg1.45932490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18522.95871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08315243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9641517
X-RAY DIFFRACTIONr_chiral_restr0.1190.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
X-RAY DIFFRACTIONr_nbd_refined0.2220.2222
X-RAY DIFFRACTIONr_nbd_other0.2170.21093
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2690
X-RAY DIFFRACTIONr_nbtor_other0.0870.2846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.232
X-RAY DIFFRACTIONr_mcbond_it2.0951.51163
X-RAY DIFFRACTIONr_mcbond_other0.6661.5363
X-RAY DIFFRACTIONr_mcangle_it2.47521464
X-RAY DIFFRACTIONr_scbond_it3.8513682
X-RAY DIFFRACTIONr_scangle_it4.7054.5575
X-RAY DIFFRACTIONr_rigid_bond_restr2.07133123
X-RAY DIFFRACTIONr_sphericity_free7.9813199
X-RAY DIFFRACTIONr_sphericity_bonded3.7532497
LS refinement shellResolution: 1.2→1.233 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 276 -
Rwork0.243 2651 -
obs-2927 92.7 %

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