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- PDB-4rcc: Crystal structure of E Coli Hfq -

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Basic information

Entry
Database: PDB / ID: 4rcc
TitleCrystal structure of E Coli Hfq
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / regulation of translation, ncRNA-mediated / RNA folding chaperone / bent DNA binding / regulation of RNA stability / regulation of DNA-templated transcription / DNA binding / 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-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsSu, J.Y.
CitationJournal: Chin J Biochem Mol Biol / Year: 2015
Title: Limited proteolysis improves E.coli Hfq crystal structure resolution
Authors: Feng, S.Q. / Si, Y.L. / Song, C.Y. / Wang, P.Q. / Su, J.Y.
History
DepositionSep 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.3Mar 20, 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
A: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)7,6541
Polymers7,6541
Non-polymers00
Water64936
1
A: RNA-binding protein Hfq
x 6


Theoretical massNumber of molelcules
Total (without water)45,9236
Polymers45,9236
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area9870 Å2
ΔGint-72 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 61.320, 28.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein RNA-binding protein Hfq / HF-1 / Host factor-I protein / HF-I


Mass: 7653.859 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-71 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A6X3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.1M TRIS.HCl pH 8.5, 1.5M Ammonium sulfate, 15 %(w/v) Glycerol, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97159 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97159 Å / Relative weight: 1
ReflectionHighest resolution: 1.98 Å / Num. obs: 4286

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.981→30.66 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 196 4.58 %
Rwork0.1802 --
obs0.1819 4277 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.981→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 0 0 36 565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008539
X-RAY DIFFRACTIONf_angle_d1.288731
X-RAY DIFFRACTIONf_dihedral_angle_d15.759204
X-RAY DIFFRACTIONf_chiral_restr0.03687
X-RAY DIFFRACTIONf_plane_restr0.00593
LS refinement shellResolution: 1.9813→30.6637 Å
RfactorNum. reflection% reflection
Rfree0.2133 196 -
Rwork0.1802 4081 -
obs--99 %

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