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- PDB-1kq2: Crystal Structure of an Hfq-RNA Complex -

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Basic information

Entry
Database: PDB / ID: 1kq2
TitleCrystal Structure of an Hfq-RNA Complex
Components
  • 5'-R(*AP*UP*UP*UP*UP*UP*G)-3'
  • Host factor for Q beta
KeywordsTRANSLATION/RNA / Hfq-RNA complex / single-stranded RNA / translational regulator / TRANSLATION-RNA COMPLEX
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / RNA-binding protein Hfq / RNA-binding protein Hfq
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsSchumacher, M.A. / Pearson, R.F. / Moller, T. / Valentin-Hansen, P. / Brennan, R.G.
CitationJournal: EMBO J. / Year: 2002
Title: Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein.
Authors: Schumacher, M.A. / Pearson, R.F. / Moller, T. / Valentin-Hansen, P. / Brennan, R.G.
History
DepositionJan 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
R: 5'-R(*AP*UP*UP*UP*UP*UP*G)-3'
A: Host factor for Q beta
B: Host factor for Q beta
H: Host factor for Q beta
I: Host factor for Q beta
K: Host factor for Q beta
M: Host factor for Q beta


Theoretical massNumber of molelcules
Total (without water)54,8807
Polymers54,8807
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.870, 115.600, 101.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsHfq is a functional hexamer and there is one hexamer bound to the 7-mer RNA site in the ASU

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Components

#1: RNA chain 5'-R(*AP*UP*UP*UP*UP*UP*G)-3'


Mass: 2160.283 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein
Host factor for Q beta / HFQ


Mass: 8786.683 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pTyb11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99UG9, UniProt: A0A0H3JV59*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 550, MgCl2, Hepes, KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 55011
2MgCl211
3Hepes11
4KCl11
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.5-1 mMHfq1
21 mMRNA1
310 %PEG550 MME12
4100 mM12KCl
515 mM12MgCl2
650 mMTris12pH7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 11, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.71→40.38 Å / Num. all: 11950 / Num. obs: 11950 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 83.4 Å2 / Rsym value: 0.064
Reflection shellResolution: 2.71→2.89 Å / % possible all: 92.1
Reflection
*PLUS
Num. measured all: 40717 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Lowest resolution: 2.8 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: one hexamer of 1KQ1

1kq1


Resolution: 2.71→40.38 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2081750.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh and huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 600 5 %RANDOM
Rwork0.204 ---
all0.204 12030 --
obs0.204 12030 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.977 Å2 / ksol: 0.323089 e/Å3
Displacement parametersBiso mean: 64.5 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---12.8 Å20 Å2
3---13.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.71→40.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 142 0 29 3156
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it2.691.5
X-RAY DIFFRACTIONc_mcangle_it4.62
X-RAY DIFFRACTIONc_scbond_it3.612
X-RAY DIFFRACTIONc_scangle_it5.482.5
LS refinement shellResolution: 2.71→2.88 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 105 5.2 %
Rwork0.315 1901 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 40.4 Å / % reflection Rfree: 5 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / Rfactor Rwork: 0.315

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