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- PDB-3gib: Crystal Structure of the Complex of the E. coli Hfq with Poly(A) -

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Basic information

Entry
Database: PDB / ID: 3gib
TitleCrystal Structure of the Complex of the E. coli Hfq with Poly(A)
Components
  • 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
  • Protein hfq
KeywordsRNA binding protein/RNA / RNA binding protein / Hfq-RNA complex / degradosome component / DNA-binding / RNA-binding / Stress response / RNA binding protein-RNA COMPLEX
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / RNA folding chaperone / regulation of translation, ncRNA-mediated / bacterial nucleoid / bent DNA binding / regulation of RNA stability / tRNA processing / tRNA binding / regulation of DNA-templated transcription ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / RNA folding chaperone / regulation of translation, ncRNA-mediated / bacterial nucleoid / bent DNA binding / regulation of RNA stability / 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 / RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLink, T.M. / Valentin-Hansen, P. / Brennan, R.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of Escherichia coli Hfq bound to polyriboadenylate RNA
Authors: Link, T.M. / Valentin-Hansen, P. / Brennan, R.G.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 1, 2017Group: Structure summary
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein hfq
B: Protein hfq
C: Protein hfq
H: 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4447
Polymers25,8234
Non-polymers6223
Water1629
1
A: Protein hfq
B: Protein hfq
C: Protein hfq
H: 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
hetero molecules

A: Protein hfq
B: Protein hfq
C: Protein hfq
H: 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,88914
Polymers51,6458
Non-polymers1,2446
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8270 Å2
ΔGint-71 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.534, 88.960, 39.635
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 7634.875 Da / Num. of mol.: 3 / Fragment: N-terminal fragment (2-69)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4172, hfq, JW4130 / Plasmid: PTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 null hfq / References: UniProt: P0A6X3
#2: RNA chain 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'


Mass: 2917.895 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 298 K / pH: 9.5
Details: 40% MPD, 0.1 M CHES 9.5, hanging drop, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2CHES11
3MPD12
4CHES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.02 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.4→89.087 Å / Num. obs: 9714 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 8.142
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.537.10.4461.7980713850.44699.8
2.53-2.6870.2992.5920513090.299100
2.68-2.8770.1614.5871312480.161100
2.87-3.170.0947.2805211530.094100
3.1-3.396.90.06110.8734910610.06199.7
3.39-3.796.90.04313.866489700.04399.9
3.79-4.386.70.04212.958588780.042100
4.38-5.376.50.04313.248497470.043100
5.37-7.5960.03514.235615970.035100
7.59-89.0960.03415.321803660.03499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å44.48 Å
Translation3.5 Å44.48 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.383 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 467 4.8 %RANDOM
Rwork0.223 ---
obs0.225 9680 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.26 Å2 / Biso mean: 61.557 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--4.32 Å2-0 Å20 Å2
2--0.33 Å20 Å2
3---3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 199 39 9 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221785
X-RAY DIFFRACTIONr_angle_refined_deg1.2232.1332470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2475188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86523.93966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31215278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8451511
X-RAY DIFFRACTIONr_chiral_restr0.0740.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021243
X-RAY DIFFRACTIONr_nbd_refined0.2040.2643
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.28
X-RAY DIFFRACTIONr_mcbond_it2.5032984
X-RAY DIFFRACTIONr_mcangle_it4.18731580
X-RAY DIFFRACTIONr_scbond_it2.2292951
X-RAY DIFFRACTIONr_scangle_it3.4953890
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 33 -
Rwork0.296 680 -
all-713 -
obs--99.72 %

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