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- PDB-1k8w: Crystal structure of the E. coli pseudouridine synthase TruB boun... -

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Basic information

Entry
Database: PDB / ID: 1k8w
TitleCrystal structure of the E. coli pseudouridine synthase TruB bound to a T stem-loop RNA
Components
  • 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'
  • tRNA Pseudouridine Synthase B
KeywordsLYASE/RNA / protein-RNA complex / T stem-loop / tRNA / LYASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA folding / tRNA pseudouridine55 synthase / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / tRNA binding / cytosol
Similarity search - Function
tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal / Pseudouridine synthase II TruB, C-terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain ...tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal / Pseudouridine synthase II TruB, C-terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain superfamily / PUA-like superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsHoang, C. / Ferre-D'Amare, A.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Authors: Hoang, C. / Ferre-D'Amare, A.R.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'
A: tRNA Pseudouridine Synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,66112
Polymers43,7012
Non-polymers96110
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.054, 40.361, 77.987
Angle α, β, γ (deg.)90.00, 110.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe T stem-loop RNA used in crystallization contains all the structural determinants employed by TruB in modifying intact tRNA

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Components

#1: RNA chain 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'


Mass: 7062.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T stem-loop RNA
#2: Protein tRNA Pseudouridine Synthase B / TruB Pseudouridine Synthase / tRNA Pseudouridine 55 Synthase / Pseudouridylate synthase


Mass: 36638.551 Da / Num. of mol.: 1 / Fragment: Residues 10-314 / Mutation: Residues 1-9 replaced with a His-Tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P60340, pseudouridylate synthase
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, magnesium chloride, peg400, hepes, tcep, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2MgCl211
3PEG 40011
4HEPES11
5TCEP11
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.21 mMprotein1drop
21.5 Mammonium sulfate1reservoir
310 mM1reservoirMgCl2
42 %PEG4001reservoir
50.1 MHEPES-KOH1reservoirpH7.5
61 mMTCEP1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9611, 0.9792, 0.9794
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJun 7, 2001monochromator
RIGAKU RAXIS IIC2IMAGE PLATEJul 4, 2001osmic confocal
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalMADMx-ray1
2osmic confocal mirrorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96111
20.97921
30.97941
41.54181
ReflectionResolution: 1.85→30 Å / Num. all: 35366 / Num. obs: 35366 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.3 Å2
Reflection shellResolution: 1.85→1.92 Å / % possible all: 94.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 107243 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 94.3 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.27 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 562571.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3444 10 %RANDOM
Rwork0.184 ---
all0.184 34482 --
obs0.184 34482 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2832 Å2 / ksol: 0.373386 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å20 Å20.08 Å2
2--5.58 Å20 Å2
3----1.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 466 50 259 3166
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.65
X-RAY DIFFRACTIONc_mcbond_it1.691.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 526 10 %
Rwork0.236 4732 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-FHP_REP.PARAMDNA-RNA-FHP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.65
X-RAY DIFFRACTIONc_mcbond_it1.691.5
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.287 / % reflection Rfree: 10 % / Rfactor Rwork: 0.236

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