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- PDB-1vio: Crystal structure of pseudouridylate synthase -

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Basic information

Entry
Database: PDB / ID: 1vio
TitleCrystal structure of pseudouridylate synthase
ComponentsRibosomal small subunit pseudouridine synthase A
KeywordsLYASE / structural genomics
Function / homology
Function and homology information


16S rRNA pseudouridine516 synthase / 16S rRNA pseudouridine(516) synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol
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 ...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 / 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 / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / Ribosomal small subunit pseudouridine synthase A
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsStructural GenomiX
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structure of the pseudouridine synthase RsuA from Haemophilus influenzae.
Authors: Matte, A. / Louie, G.V. / Sivaraman, J. / Cygler, M. / Burley, S.K.
#1: Journal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Category: citation_author / struct_site
Item: _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal small subunit pseudouridine synthase A
B: Ribosomal small subunit pseudouridine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3106
Polymers54,9502
Non-polymers3604
Water9,512528
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.163, 76.973, 62.771
Angle α, β, γ (deg.)90.00, 108.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal small subunit pseudouridine synthase A / 16S pseudouridylate 516 synthase / 16S pseudouridine 516 synthase / Uracil hydrolyase


Mass: 27474.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: RSUA, HI1243 / Production host: Escherichia coli (E. coli) / References: UniProt: P45124, pseudouridylate synthase
#2: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-30 mg/mlprotein1drop
210 mMHEPES1droppH7.5
3150 mM1dropNaCl
410 mMmethionine1drop
510 %(v/v)glycerol1drop
61 mMbeta-mercaptoethanol1drop
72.0 Mammonium sulfate1reservoir
80.1 Msodium acetate1reservoirpH4.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.51→22.14 Å / Num. all: 80022 / Num. obs: 80022 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.5
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.01109 / Mean I/σ(I) obs: 1.8 / % possible all: 97.4
Reflection
*PLUS
Lowest resolution: 22 Å / Num. obs: 80195 / Num. measured all: 587441
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→22.14 Å / σ(F): 0
RfactorNum. reflection
Rfree0.218 3437
Rwork0.196 -
obs-69152
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 165.646 Å2 / ksol: 0.783 e/Å3
Displacement parametersBiso mean: 21.208 Å2
Baniso -1Baniso -2Baniso -3
1--0.546 Å20 Å2-0.473 Å2
2--0.751 Å20 Å2
3----0.509 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.59→22.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 24 528 4208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.004
X-RAY DIFFRACTIONp_angle_d1.448
X-RAY DIFFRACTIONp_planar_tor1.543
X-RAY DIFFRACTIONp_chiral_restr0.102
X-RAY DIFFRACTIONp_plane_restr0.007
X-RAY DIFFRACTIONp_mcbond_it1.997
X-RAY DIFFRACTIONp_mcangle_it3.377
X-RAY DIFFRACTIONp_scbond_it3.822
X-RAY DIFFRACTIONp_scangle_it5.958
Software
*PLUS
Version: 4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 22.1 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 1.45
LS refinement shell
*PLUS
Num. reflection Rfree: 3437 / Num. reflection Rwork: 65715

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