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- PDB-1zl3: Coupling of active site motions and RNA binding -

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Basic information

Entry
Database: PDB / ID: 1zl3
TitleCoupling of active site motions and RNA binding
Components
  • 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FLO) UP*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'
  • tRNA pseudouridine synthase B
KeywordsLYASE/RNA / RNA-modification / inter-domain coupling / product release / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHoang, C. / Hamilton, C.S. / Mueller, E.G. / Ferre-D'Amare, A.R.
CitationJournal: Protein Sci. / Year: 2005
Title: Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain
Authors: Hoang, C. / Hamilton, C.S. / Mueller, E.G. / Ferre-D'Amare, A.R.
History
DepositionMay 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FLO) UP*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)43,9545
Polymers43,6662
Non-polymers2883
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.433, 40.753, 78.803
Angle α, β, γ (deg.)90.00, 110.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 7028.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T-STEM LOOP RNA
#2: Protein tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate ...tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate synthase / Protein p35


Mass: 36637.566 Da / Num. of mol.: 1 / Mutation: D48N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: truB / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60340, pseudouridylate synthase
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.5 Å3/Da / Density % sol: 0.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate [1.7M], PEG400 [2%], Hepes-KOH pH 7.5 [0.1M] and TCEP [1 mM], pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2002
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 10935 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 6.34 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 23.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.71 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.341 / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K8W

1k8w


Resolution: 2.8→19.92 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1083 9.9 %RANDOM
Rwork0.202 ---
all0.202 ---
obs0.202 10935 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.18 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 50.7 Å2
Baniso -1Baniso -2Baniso -3
1--16.68 Å20 Å20.35 Å2
2--28.39 Å20 Å2
3----11.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 465 15 26 2831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4332 94 8.63 %
Rwork0.3432 988 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-5FU_REP.PARAMDNA-RNA-5FU.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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