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- PDB-4jri: Crystal Structure of Escherichia coli Hfq Proximal Edge Mutant -

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Basic information

Entry
Database: PDB / ID: 4jri
TitleCrystal Structure of Escherichia coli Hfq Proximal Edge Mutant
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / Riboregulator / Post-transcriptional regulator
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription / DNA binding / RNA binding / ATP 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: 1.829 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 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 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


Theoretical massNumber of molelcules
Total (without water)30,6964
Polymers30,6964
Non-polymers00
Water2,306128
1
A: Protein hfq
B: Protein hfq

A: Protein hfq
B: Protein hfq

A: Protein hfq
B: Protein hfq


Theoretical massNumber of molelcules
Total (without water)46,0436
Polymers46,0436
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area8840 Å2
ΔGint-77 kcal/mol
Surface area17310 Å2
MethodPISA
2
C: Protein hfq
D: Protein hfq

C: Protein hfq
D: Protein hfq

C: Protein hfq
D: Protein hfq


Theoretical massNumber of molelcules
Total (without water)46,0436
Polymers46,0436
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544z+1/2,-x-1/2,-y-11
crystal symmetry operation12_444-y-1/2,-z-1,x-1/21
Buried area8860 Å2
ΔGint-78 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.087, 90.087, 90.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-117-

HOH

21B-118-

HOH

31B-129-

HOH

41D-112-

HOH

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Components

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


Mass: 7673.911 Da / Num. of mol.: 4 / Fragment: UNP residues 2-69 / Mutation: F39W
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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.98 Å3/Da / Density % sol: 38.03 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.829→24.077 Å / Num. obs: 21700 / Rsym value: 0.06

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.829→24.077 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 26.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2573 1105 5.09 %
Rwork0.2052 --
obs0.2078 21700 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.829→24.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 0 128 2183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082205
X-RAY DIFFRACTIONf_angle_d1.2073031
X-RAY DIFFRACTIONf_dihedral_angle_d14.857869
X-RAY DIFFRACTIONf_chiral_restr0.087365
X-RAY DIFFRACTIONf_plane_restr0.005385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8294-1.91260.29841390.25952531X-RAY DIFFRACTION99
1.9126-2.01340.27791380.24142548X-RAY DIFFRACTION100
2.0134-2.13950.35681130.23832584X-RAY DIFFRACTION100
2.1395-2.30450.23561410.21472562X-RAY DIFFRACTION100
2.3045-2.53620.2721500.21662552X-RAY DIFFRACTION100
2.5362-2.90270.26161270.21342608X-RAY DIFFRACTION100
2.9027-3.6550.22961420.19962592X-RAY DIFFRACTION100
3.655-24.07880.25421550.18582618X-RAY DIFFRACTION98

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