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- PDB-4qvd: E.coli Hfq in complex with RNA Ads -

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Basic information

Entry
Database: PDB / ID: 4qvd
TitleE.coli Hfq in complex with RNA Ads
Components
  • RNA (5'-R(*AP*AP*CP*UP*AP*AP*A)-3')
  • RNA-binding protein Hfq
KeywordsRNA binding protein/RNA / SM fold / RNA chaperone / RNA / RNA binding protein-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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 Å
AuthorsWang, L.J. / Wang, W.W. / Li, F.D. / Wu, J.H. / Gong, Q.G. / Shi, Y.Y.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq
Authors: Wang, L.J. / Wang, W.W. / Li, F.D. / Zhang, J. / Wu, J.H. / Gong, Q.G. / Shi, Y.Y.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
H: RNA (5'-R(*AP*AP*CP*UP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)46,1667
Polymers46,1667
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.280, 68.270, 111.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RNA-binding protein Hfq


Mass: 7325.554 Da / Num. of mol.: 6 / Fragment: UNP residues 1-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hfq / Production host: Escherichia coli (E. coli) / References: UniProt: C1IFD2
#2: RNA chain RNA (5'-R(*AP*AP*CP*UP*AP*AP*A)-3')


Mass: 2212.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in E.coli. / Source: (synth.) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 16% MPEG5000, 0.1M Hepes, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2012
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.972→58.19 Å / Num. all: 32548 / Num. obs: 29189 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.972→2.08 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 7.7 / % possible all: 91.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HK9

1hk9


Resolution: 1.972→34.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.468 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22923 1464 5 %RANDOM
Rwork0.18479 ---
obs0.18699 27725 89.68 %-
all-32548 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.311 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.972→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 85 0 235 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193020
X-RAY DIFFRACTIONr_bond_other_d0.0010.022975
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9454118
X-RAY DIFFRACTIONr_angle_other_deg0.73936816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74524.754122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78515520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8581514
X-RAY DIFFRACTIONr_chiral_restr0.070.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.972→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 108 -
Rwork0.218 2173 -
obs--96.12 %

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