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- PDB-4juv: Crystal Structure of Escherichia coli Hfq Distal Face 1 Mutant -

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Basic information

Entry
Database: PDB / ID: 4juv
TitleCrystal Structure of Escherichia coli Hfq Distal Face 1 Mutant
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / Hfq / Riboregulator / POst-transcriptional regulator
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsRobinson, K.E. / Orans, J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching.
Authors: Robinson, K.E. / Orans, J. / Kovach, A.R. / Link, T.M. / Brennan, R.G.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein hfq
B: Protein hfq
C: Protein hfq
D: Protein hfq
E: Protein hfq
F: Protein hfq


Theoretical massNumber of molelcules
Total (without water)45,9476
Polymers45,9476
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-70 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.630, 89.148, 66.987
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein hfq / HF-1 / Host factor-I protein / HF-I


Mass: 7657.911 Da / Num. of mol.: 6 / Mutation: Y25W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hfq, b4172, JW4130 / References: UniProt: P0A6X3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.06 Å3/Da / Density % sol: 40.16 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.19→44.61 Å / Num. obs: 18462 / Rsym value: 0.041

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Processing

Software
NameVersionClassification
HKL-3000data collection
CCP4model building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→44.61 Å / Cor.coef. Fo:Fc: 0.928 / ESU R: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rwork0.26372 --
obs0.26372 18462 96.6 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.524 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å20 Å2-0.23 Å2
2--0.28 Å2-0 Å2
3----4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 0 75 3124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193129
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.964254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68723.75136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28215562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9451524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212300
LS refinement shellHighest resolution: 2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 0 -
Rwork0.26 1184 -
obs--82.34 %

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