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- PDB-1prz: Crystal structure of pseudouridine synthase RluD catalytic module -

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Basic information

Entry
Database: PDB / ID: 1prz
TitleCrystal structure of pseudouridine synthase RluD catalytic module
ComponentsRibosomal large subunit pseudouridine synthase D
KeywordsLYASE / Pseudouridine synthase / RluD / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
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 / ribosomal large subunit assembly / rRNA binding / RNA binding / cytoplasm / 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 - #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 / Ribosomal large subunit pseudouridine synthase D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsSivaraman, J. / Iannuzzi, P. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of the RluD pseudouridine Synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli
Authors: Sivaraman, J. / Iannuzzi, P. / Cygler, M. / Matte, A.
History
DepositionJun 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)29,2291
Polymers29,2291
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.261, 76.362, 85.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Ribosomal large subunit pseudouridine synthase D / E.C.4.2.1.70 / Pseudouridylate synthase / Uracil hydrolyase / suppressor of ftsH mutation


Mass: 29229.068 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 or SFHB / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: Q8X9F0, UniProt: P33643*PLUS, pseudouridylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7
Details: PEG 8000, KCL, Glycerol, pH 7., microbatch under oil, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
114 %(w/v)PEG800012
2550 mM12KCl
312 %glycerol12
414 mg/mlprotein11
520 mMTris-HCl11pH8.
6200 mM11NaCl
710 mMdithiothreitol11
85 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Feb 24, 2003
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 32444 / Num. obs: 32444 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Rsym value: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.86 Å / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 107285 / Rmerge(I) obs: 0.065

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Processing

Software
NameVersionClassification
CRYSATLCLEARdata collection
HKL-2000data reduction
SOLVEphasing
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2406 8 %RANDAM
Rwork0.218 ---
all-32444 --
obs-29910 --
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 0 294 2315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 45 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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