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- PDB-1ksk: STRUCTURE OF RSUA -

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Basic information

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


16S rRNA pseudouridine516 synthase / 16S rRNA pseudouridine(516) synthase activity / 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, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase / Pseudouridine synthase ...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, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / 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
URACIL / Ribosomal small subunit pseudouridine synthase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 13, 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 / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 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 / struct_sheet / struct_site
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 / _struct_sheet.number_strands / _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 SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4832
Polymers26,3711
Non-polymers1121
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.771, 149.220, 35.200
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-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 3350, Malate, KSCN, Isoproponal, Glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114-16 %(w/v)PEG33501reservoir
2100 mMmalate1reservoirpH5.6
3100 mM1reservoirKSCN
418 %isopropanol1reservoir
52-5 %(w/v)glycerol1reservoir
617 mg/mlprotein1drop
720 mMTris-HCl1droppH7.5
8200 mM1dropNaCl
95 %(w/v)glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.968634 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2001
RadiationMonochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968634 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 31168 / Num. obs: 31168 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.235 / % possible all: 61.9
Reflection
*PLUS
Num. measured all: 103836 / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
Adxvdata processing
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→45 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2089 -RANDOM
Rwork0.217 ---
all-30730 --
obs-30730 91.5 %-
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 8 222 2058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008368
X-RAY DIFFRACTIONc_angle_d1.41234
X-RAY DIFFRACTIONc_improper_angle_d1.02
Refinement
*PLUS
Rfactor all: 0.262 / Rfactor obs: 0.217 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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