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- PDB-4qvc: E.coli Hfq in complex with RNA Aus -

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Basic information

Entry
Database: PDB / ID: 4qvc
TitleE.coli Hfq in complex with RNA Aus
Components
  • RNA (5'-R(*AP*U*AP*AP*CP*UP*A)-3')
  • RNA-binding protein Hfq
KeywordsRNA binding protein/RNA / SM fold / RNA binding / 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: 1.99 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 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 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
G: RNA (5'-R(*AP*U*AP*AP*CP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)46,1437
Polymers46,1437
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.236, 67.989, 111.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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*U*AP*AP*CP*UP*A)-3')


Mass: 2189.379 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.: 183 / 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: 2.43 Å3/Da / Density % sol: 49.3 % / Mosaicity: 0.554 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG4000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2013
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.99→40 Å / Num. all: 31605 / Num. obs: 29582 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.105 / Χ2: 1.331 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.078.40.51231101.03399.9
2.07-2.158.40.41830961.22399.9
2.15-2.257.60.44626641.46585.8
2.25-2.377.60.35623061.59473.8
2.37-2.528.50.20131371.187100
2.52-2.718.60.17431331.384100
2.71-2.998.60.13631471.513100
2.99-3.428.50.131621.484100
3.42-4.316.30.06625341.30178.7
4.31-407.90.04932931.22197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HK9

1hk9


Resolution: 1.99→33.99 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2629 / WRfactor Rwork: 0.2141 / FOM work R set: 0.8037 / SU B: 4.6 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1964 / SU Rfree: 0.1745 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 1471 5 %RANDOM
Rwork0.2111 ---
all0.2132 31605 --
obs0.2132 29409 93.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.64 Å2 / Biso mean: 34.715 Å2 / Biso min: 16.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.99→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 64 0 183 3119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192991
X-RAY DIFFRACTIONr_bond_other_d0.0010.022981
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9534070
X-RAY DIFFRACTIONr_angle_other_deg0.77336822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26524.59122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32115524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.391515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_mcbond_it2.2753.3371450
X-RAY DIFFRACTIONr_mcbond_other2.2743.3361449
X-RAY DIFFRACTIONr_mcangle_it3.444.981802
LS refinement shellResolution: 1.988→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 108 -
Rwork0.276 2126 -
all-2234 -
obs--96.71 %

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