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- PDB-1p6v: Crystal structure of the tRNA domain of transfer-messenger RNA in... -

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Basic information

Entry
Database: PDB / ID: 1p6v
TitleCrystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB
Components
  • 45-MER
  • SsrA-binding protein
KeywordsRNA BINDING PROTEIN/RNA / SmpB / tmRNA / trans-translation / protein-RNA complex / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


trans-translation / RNA binding / cytosol
Similarity search - Function
Small Protein B; Chain: A; / Small protein B / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / SsrA-binding protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsGutmann, S. / Haebel, P.W. / Metzinger, L. / Sutter, M. / Felden, B. / Ban, N.
CitationJournal: Nature / Year: 2003
Title: Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB
Authors: Gutmann, S. / Haebel, P.W. / Metzinger, L. / Sutter, M. / Felden, B. / Ban, N.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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

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Assembly

Deposited unit
B: 45-MER
D: 45-MER
A: SsrA-binding protein
C: SsrA-binding protein


Theoretical massNumber of molelcules
Total (without water)80,8004
Polymers80,8004
Non-polymers00
Water0
1
B: 45-MER
A: SsrA-binding protein


Theoretical massNumber of molelcules
Total (without water)40,4002
Polymers40,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 45-MER
C: SsrA-binding protein


Theoretical massNumber of molelcules
Total (without water)40,4002
Polymers40,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.680, 99.680, 207.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsSmpB (chain A) and tmRNA[delta] (chain B) for the ribonucleoprotein complex / SmpB (chain C) and tmRNA[delta] (chain D) for the ribonucleoprotein complex; poorer defined in electron density

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Components

#1: RNA chain 45-MER


Mass: 21959.070 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: In vitro transcription of Aquifex aeolicus tmRNA[delta]
#2: Protein SsrA-binding protein


Mass: 18440.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: SMPB / Production host: Escherichia coli (E. coli) / References: UniProt: O66640

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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: 5.22 Å3/Da / Density % sol: 76.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Isopropanol, cacodylate, ammonium acetate, magnesium acetate, calcium acetate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Isopropanol11
2cacodylateCacodylic acid11
3ammonium acetate11
4magnesium acetate11
5calcium acetate11
6H2O11
7cacodylateCacodylic acid12
8magnesium acetate12
9calcium acetate12
10H2O12
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
210 %2-propanol1reservoir
3100 mMmagnesium acetate1reservoir
415 mMammonium acetate1reservoir
550 mMsodium cacodylate1reservoirpH6.8
60.2 mMgentamicin1reservoiror neomycin B
716 mM1reservoirCaCl2
81
91
101

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.008 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 17756 / Num. obs: 17756 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.07 / Net I/σ(I): 23.1
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.87 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.873

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→19.94 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: GROUPED B-Factors / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.36 1647 9.8 %RANDOM
Rwork0.302 ---
obs0.302 16854 94.4 %-
all-18501 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 90.774 Å2 / ksol: 0.224974 e/Å3
Displacement parametersBiso mean: 108.4 Å2
Baniso -1Baniso -2Baniso -3
1-15.09 Å20 Å20 Å2
2--15.09 Å20 Å2
3----30.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 1465 0 0 3519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.36
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.46 212 8.3 %
Rwork0.413 2332 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.TOP
X-RAY DIFFRACTION4ION.TOP
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.36
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.36

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