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- PDB-2y90: Crystal structure of Hfq riboregulator from E. coli (P6 space group) -

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Basic information

Entry
Database: PDB / ID: 2y90
TitleCrystal structure of Hfq riboregulator from E. coli (P6 space group)
ComponentsPROTEIN HFQ
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / SM-LIKE / RNA CHAPERONE
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: 2.252 Å
AuthorsBasquin, J. / Sauter, C.
Citation
Journal: Cryst. Growth Des. / Year: 2011
Title: Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination
Authors: Bonnefond, L. / Schellenberger, P. / Basquin, J. / Demangeat, G. / Ritzenthaler, C. / Chenevert, R. / Balg, C. / Frugier, M. / Rudinger-Thirion, J. / Giege, R. / Lorber, L. / Sauter, C.
#1: Journal: Nucleic Acids Res. / Year: 2003
Title: Sm-Like Proteins in Eubacteria: The Crystal Structure of the Hfq Protein from Escherichia Coli.
Authors: Sauter, C. / Basquin, J. / Suck, D.
History
DepositionFeb 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN HFQ


Theoretical massNumber of molelcules
Total (without water)11,3071
Polymers11,3071
Non-polymers00
Water19811
1
A: PROTEIN HFQ
x 6


Theoretical massNumber of molelcules
Total (without water)67,8456
Polymers67,8456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_555y,-x+y,z1
Buried area8520 Å2
ΔGint-71.1 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.500, 61.500, 28.250
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 PROTEIN HFQ / HF-1 / HOST FACTOR-I PROTEIN / HF-I


Mass: 11307.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: P0A6X3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTWO AMINO ACIDS ADDED IN N-TERMINUS AND PROBABLE PROTEOLYTIC DEGRADATION AFTER RESIDUE 69. RESIDUES ...TWO AMINO ACIDS ADDED IN N-TERMINUS AND PROBABLE PROTEOLYTIC DEGRADATION AFTER RESIDUE 69. RESIDUES 70-102 ARE EITHER DISORDERED IN THE CRYSTAL OR ABSENT DUE TO PROTEOLYSIS.

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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: 1.7 Å3/Da / Density % sol: 30 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL HANGING DROPS AT 20C. THE RESERVOIR CONTAINED 1.6 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 8.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.313
ReflectionResolution: 2.25→54 Å / Num. obs: 2979 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7
Reflection shellResolution: 2.25→2.3 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.3 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 2.252→53.261 Å / σ(F): 0 / Phase error: 32.43 / Stereochemistry target values: TWIN_LSQ_F
Details: THE FULL LENGTH HFQ PROTEIN CRYSTALLIZED AFTER PROTEOLYTIC DEGRADATION AS INDICATED BY THE CRYSTAL SOLVENT SOLVENT CONTENT (SEE REF1). THE RESULTING MONOMER LACKS RESIDUES 70-102. THE LATTER ...Details: THE FULL LENGTH HFQ PROTEIN CRYSTALLIZED AFTER PROTEOLYTIC DEGRADATION AS INDICATED BY THE CRYSTAL SOLVENT SOLVENT CONTENT (SEE REF1). THE RESULTING MONOMER LACKS RESIDUES 70-102. THE LATTER ARE EITHER DISORDERED IN THE CRYSTAL OR ABSENT DUE TO BY PROTEOLYSIS.
RfactorNum. reflection% reflection
Rfree0.2258 232 7.8 %
Rwork0.1798 --
obs0.1881 2979 99.04 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.035 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.664 Å2-0 Å20 Å2
2---2.664 Å20 Å2
3---5.3279 Å2
Refinement stepCycle: LAST / Resolution: 2.252→53.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms510 0 0 11 521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007519
X-RAY DIFFRACTIONf_angle_d1.164704
X-RAY DIFFRACTIONf_dihedral_angle_d14.25197
X-RAY DIFFRACTIONf_chiral_restr0.07785
X-RAY DIFFRACTIONf_plane_restr0.00589
LS refinement shellResolution: 2.2608→24.9582 Å
RfactorNum. reflection% reflection
Rfree0.2262 232 -
Rwork0.1832 2713 -
obs--91 %

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